Author: "Xu, Qingping" / Database: OAIster - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Xu, Qingping"' showing total 48 results

Start Over Author "Xu, Qingping" Database OAIster

48 results on '"Xu, Qingping"'

1. Retraction: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50, William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik.

Author: Hwang, William C, Hwang, William C, Xu, Qingping, Wu, Bainan, Godzik, Adam, Hwang, William C, Hwang, William C, Xu, Qingping, Wu, Bainan, and Godzik, Adam
Abstract: The above article from Proteins: Structure, Function, and Bioinformatics, published online on 5 August 2014 in Wiley Online Library (http://onlinelibrary.wiley.com/doi/10.1002/prot.24661/full), has been retracted by agreement between William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik, the Editor‐in‐Chief, Bertrand E. Garcia‐Moreno, and Wiley Periodicals, Inc. The retraction has been agreed because submission was made without agreement from co‐author Adam Godzik.
Published: 2018

2. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

Author: Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution), have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.
Published: 2011

3. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites.

Author: Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.
Published: 2011

4. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites.

Author: Xu, Qingping, Sussman, Joel L1, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Sussman, Joel L1, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.
Published: 2011

5. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

Author: Xu, Qingping, Rodrigues-Lima, Fernando1, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Rodrigues-Lima, Fernando1, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution), have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.
Published: 2011

6. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.

Author: Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.
Published: 2010

7. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution.

Author: Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in Porphyromonas gingivalis. The crystal structure of BT1062 revealed a conserved fold that is widely adopted by fimbrial components.
Published: 2010

8. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution.

Author: Xu, Qingping, Xu, Qingping, McMullan, Daniel, Jaroszewski, Lukasz, Krishna, S Sri, Elsliger, Marc André, Yeh, Andrew P, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna, Han, Gye Won, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, McMullan, Daniel, Jaroszewski, Lukasz, Krishna, S Sri, Elsliger, Marc André, Yeh, Andrew P, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna, Han, Gye Won, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.
Published: 2010

9. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.

Author: Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.
Published: 2010

10. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution.

Author: Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in Porphyromonas gingivalis. The crystal structure of BT1062 revealed a conserved fold that is widely adopted by fimbrial components.
Published: 2010

11. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution.

Author: Xu, Qingping, Xu, Qingping, McMullan, Daniel, Jaroszewski, Lukasz, Krishna, S Sri, Elsliger, Marc André, Yeh, Andrew P, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna, Han, Gye Won, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, McMullan, Daniel, Jaroszewski, Lukasz, Krishna, S Sri, Elsliger, Marc André, Yeh, Andrew P, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna, Han, Gye Won, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.
Published: 2010

12. Visualizing chaperone-assisted protein folding.

Author: Horowitz, Scott, Horowitz, Scott, Salmon, Loïc, Koldewey, Philipp, Ahlstrom, Logan S, Martin, Raoul, Quan, Shu, Afonine, Pavel V, van den Bedem, Henry, Wang, Lili, Xu, Qingping, Trievel, Raymond C, Brooks, Charles L, Bardwell, James CA, Horowitz, Scott, Horowitz, Scott, Salmon, Loïc, Koldewey, Philipp, Ahlstrom, Logan S, Martin, Raoul, Quan, Shu, Afonine, Pavel V, van den Bedem, Henry, Wang, Lili, Xu, Qingping, Trievel, Raymond C, Brooks, Charles L, and Bardwell, James CA
Abstract: Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.
Published: 2016

13. Visualizing chaperone-assisted protein folding.

Author: Horowitz, Scott, Horowitz, Scott, Salmon, Loïc, Koldewey, Philipp, Ahlstrom, Logan S, Martin, Raoul, Quan, Shu, Afonine, Pavel V, van den Bedem, Henry, Wang, Lili, Xu, Qingping, Trievel, Raymond C, Brooks, Charles L, Bardwell, James CA, Horowitz, Scott, Horowitz, Scott, Salmon, Loïc, Koldewey, Philipp, Ahlstrom, Logan S, Martin, Raoul, Quan, Shu, Afonine, Pavel V, van den Bedem, Henry, Wang, Lili, Xu, Qingping, Trievel, Raymond C, Brooks, Charles L, and Bardwell, James CA
Abstract: Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.
Published: 2016

14. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

Author: Kang, Yanyong, Kang, Yanyong, Zhou, X Edward, Gao, Xiang, He, Yuanzheng, Liu, Wei, Ishchenko, Andrii, Barty, Anton, White, Thomas A, Yefanov, Oleksandr, Han, Gye Won, Xu, Qingping, de Waal, Parker W, Ke, Jiyuan, Tan, MH Eileen, Zhang, Chenghai, Moeller, Arne, West, Graham M, Pascal, Bruce D, Van Eps, Ned, Caro, Lydia N, Vishnivetskiy, Sergey A, Lee, Regina J, Suino-Powell, Kelly M, Gu, Xin, Pal, Kuntal, Ma, Jinming, Zhi, Xiaoyong, Boutet, Sébastien, Williams, Garth J, Messerschmidt, Marc, Gati, Cornelius, Zatsepin, Nadia A, Wang, Dingjie, James, Daniel, Basu, Shibom, Roy-Chowdhury, Shatabdi, Conrad, Chelsie E, Coe, Jesse, Liu, Haiguang, Lisova, Stella, Kupitz, Christopher, Grotjohann, Ingo, Fromme, Raimund, Jiang, Yi, Tan, Minjia, Yang, Huaiyu, Li, Jun, Wang, Meitian, Zheng, Zhong, Li, Dianfan, Howe, Nicole, Zhao, Yingming, Standfuss, Jörg, Diederichs, Kay, Dong, Yuhui, Potter, Clinton S, Carragher, Bridget, Caffrey, Martin, Jiang, Hualiang, Chapman, Henry N, Spence, John CH, Fromme, Petra, Weierstall, Uwe, Ernst, Oliver P, Katritch, Vsevolod, Gurevich, Vsevolod V, Griffin, Patrick R, Hubbell, Wayne L, Stevens, Raymond C, Cherezov, Vadim, Melcher, Karsten, Xu, H Eric, Kang, Yanyong, Kang, Yanyong, Zhou, X Edward, Gao, Xiang, He, Yuanzheng, Liu, Wei, Ishchenko, Andrii, Barty, Anton, White, Thomas A, Yefanov, Oleksandr, Han, Gye Won, Xu, Qingping, de Waal, Parker W, Ke, Jiyuan, Tan, MH Eileen, Zhang, Chenghai, Moeller, Arne, West, Graham M, Pascal, Bruce D, Van Eps, Ned, Caro, Lydia N, Vishnivetskiy, Sergey A, Lee, Regina J, Suino-Powell, Kelly M, Gu, Xin, Pal, Kuntal, Ma, Jinming, Zhi, Xiaoyong, Boutet, Sébastien, Williams, Garth J, Messerschmidt, Marc, Gati, Cornelius, Zatsepin, Nadia A, Wang, Dingjie, James, Daniel, Basu, Shibom, Roy-Chowdhury, Shatabdi, Conrad, Chelsie E, Coe, Jesse, Liu, Haiguang, Lisova, Stella, Kupitz, Christopher, Grotjohann, Ingo, Fromme, Raimund, Jiang, Yi, Tan, Minjia, Yang, Huaiyu, Li, Jun, Wang, Meitian, Zheng, Zhong, Li, Dianfan, Howe, Nicole, Zhao, Yingming, Standfuss, Jörg, Diederichs, Kay, Dong, Yuhui, Potter, Clinton S, Carragher, Bridget, Caffrey, Martin, Jiang, Hualiang, Chapman, Henry N, Spence, John CH, Fromme, Petra, Weierstall, Uwe, Ernst, Oliver P, Katritch, Vsevolod, Gurevich, Vsevolod V, Griffin, Patrick R, Hubbell, Wayne L, Stevens, Raymond C, Cherezov, Vadim, Melcher, Karsten, and Xu, H Eric
Abstract: G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.
Published: 2015

15. Structure of the angiotensin receptor revealed by serial femtosecond crystallography

Author: Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., Cherezov, Vadim, Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., and Cherezov, Vadim
Abstract: Angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT1R-ZD7155 complex structure revealed key structural features of AT1R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.
Published: 2015

16. Structure of the angiotensin receptor revealed by serial femtosecond crystallography

Author: Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., Cherezov, Vadim, Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., and Cherezov, Vadim
Abstract: Angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT1R-ZD7155 complex structure revealed key structural features of AT1R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.
Published: 2015

17. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

Author: Kang, Yanyong, Kang, Yanyong, Zhou, X Edward, Gao, Xiang, He, Yuanzheng, Liu, Wei, Ishchenko, Andrii, Barty, Anton, White, Thomas A, Yefanov, Oleksandr, Han, Gye Won, Xu, Qingping, de Waal, Parker W, Ke, Jiyuan, Tan, MH Eileen, Zhang, Chenghai, Moeller, Arne, West, Graham M, Pascal, Bruce D, Van Eps, Ned, Caro, Lydia N, Vishnivetskiy, Sergey A, Lee, Regina J, Suino-Powell, Kelly M, Gu, Xin, Pal, Kuntal, Ma, Jinming, Zhi, Xiaoyong, Boutet, Sébastien, Williams, Garth J, Messerschmidt, Marc, Gati, Cornelius, Zatsepin, Nadia A, Wang, Dingjie, James, Daniel, Basu, Shibom, Roy-Chowdhury, Shatabdi, Conrad, Chelsie E, Coe, Jesse, Liu, Haiguang, Lisova, Stella, Kupitz, Christopher, Grotjohann, Ingo, Fromme, Raimund, Jiang, Yi, Tan, Minjia, Yang, Huaiyu, Li, Jun, Wang, Meitian, Zheng, Zhong, Li, Dianfan, Howe, Nicole, Zhao, Yingming, Standfuss, Jörg, Diederichs, Kay, Dong, Yuhui, Potter, Clinton S, Carragher, Bridget, Caffrey, Martin, Jiang, Hualiang, Chapman, Henry N, Spence, John CH, Fromme, Petra, Weierstall, Uwe, Ernst, Oliver P, Katritch, Vsevolod, Gurevich, Vsevolod V, Griffin, Patrick R, Hubbell, Wayne L, Stevens, Raymond C, Cherezov, Vadim, Melcher, Karsten, Xu, H Eric, Kang, Yanyong, Kang, Yanyong, Zhou, X Edward, Gao, Xiang, He, Yuanzheng, Liu, Wei, Ishchenko, Andrii, Barty, Anton, White, Thomas A, Yefanov, Oleksandr, Han, Gye Won, Xu, Qingping, de Waal, Parker W, Ke, Jiyuan, Tan, MH Eileen, Zhang, Chenghai, Moeller, Arne, West, Graham M, Pascal, Bruce D, Van Eps, Ned, Caro, Lydia N, Vishnivetskiy, Sergey A, Lee, Regina J, Suino-Powell, Kelly M, Gu, Xin, Pal, Kuntal, Ma, Jinming, Zhi, Xiaoyong, Boutet, Sébastien, Williams, Garth J, Messerschmidt, Marc, Gati, Cornelius, Zatsepin, Nadia A, Wang, Dingjie, James, Daniel, Basu, Shibom, Roy-Chowdhury, Shatabdi, Conrad, Chelsie E, Coe, Jesse, Liu, Haiguang, Lisova, Stella, Kupitz, Christopher, Grotjohann, Ingo, Fromme, Raimund, Jiang, Yi, Tan, Minjia, Yang, Huaiyu, Li, Jun, Wang, Meitian, Zheng, Zhong, Li, Dianfan, Howe, Nicole, Zhao, Yingming, Standfuss, Jörg, Diederichs, Kay, Dong, Yuhui, Potter, Clinton S, Carragher, Bridget, Caffrey, Martin, Jiang, Hualiang, Chapman, Henry N, Spence, John CH, Fromme, Petra, Weierstall, Uwe, Ernst, Oliver P, Katritch, Vsevolod, Gurevich, Vsevolod V, Griffin, Patrick R, Hubbell, Wayne L, Stevens, Raymond C, Cherezov, Vadim, Melcher, Karsten, and Xu, H Eric
Abstract: G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.
Published: 2015

18. Structure of the angiotensin receptor revealed by serial femtosecond crystallography

Author: Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., Cherezov, Vadim, Zhang, Haitao, Unal, Hamiyet, Gati, Cornelius, Han, Gye Won, Liu, Wei, Zatsepin, Nadia A., James, Daniel, Wang, Dingjie, Nelson, Garrett, Weierstall, Uwe, Sawaya, Michael R., Xu, Qingping, Messerschmidt, Marc, Williams, Garth J., Boutet, Sébastien, Yefanov, Oleksandr M., White, Thomas A., Wang, Chong, Ishchenko, Andrii, Tirupula, Kalyan C., Desnoyer, Russell, Coe, Jesse, Conrad, Chelsie E., Fromme, Petra, Stevens, Raymond C., Katritch, Vsevolod, Karnik, Sadashiva S., and Cherezov, Vadim
Abstract: Angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT1R-ZD7155 complex structure revealed key structural features of AT1R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.
Published: 2015

19. Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.

Author: Fleischman, Nicholas M, Fleischman, Nicholas M, Das, Debanu, Kumar, Abhinav, Xu, Qingping, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Knuth, Mark W, Klock, Heath E, Miller, Mitchell D, Elsliger, Marc-André, Godzik, Adam, Lesley, Scott A, Deacon, Ashley M, Wilson, Ian A, Toney, Michael D, Fleischman, Nicholas M, Fleischman, Nicholas M, Das, Debanu, Kumar, Abhinav, Xu, Qingping, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Knuth, Mark W, Klock, Heath E, Miller, Mitchell D, Elsliger, Marc-André, Godzik, Adam, Lesley, Scott A, Deacon, Ashley M, Wilson, Ian A, and Toney, Michael D
Abstract: Pyridoxal-5'-phosphate or PLP, the active form of vitamin B6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. PLP-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. Here, we structurally and functionally characterize three novel PLP-dependent enzymes from bacteria in the human microbiome: two are from Eubacterium rectale, a dominant, nonpathogenic, fecal, Gram-positive bacteria, and the third is from Porphyromonas gingivalis, which plays a major role in human periodontal disease. All adopt the Type I PLP-dependent enzyme fold and structure-guided biochemical analysis enabled functional assignments as tryptophan, aromatic, and probable phosphoserine aminotransferases.
Published: 2014

20. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin

Author: Xu, Qingping, Deller, Marc C, Nielsen, Tine K, Grant, Joanna C, Lesley, Scott A, Elsliger, Marc-André, Deacon, Ashley M, Wilson, Ian A, Xu, Qingping, Deller, Marc C, Nielsen, Tine K, Grant, Joanna C, Lesley, Scott A, Elsliger, Marc-André, Deacon, Ashley M, and Wilson, Ian A
Abstract: Kanadaptin is a nuclear protein of unknown function that is widely expressed in mammalian tissues. The crystal structure of the forkhead-associated (FHA) domain of human kanadaptin was determined to 1.6 Å resolution. The structure reveals an asymmetric dimer in which one monomer is complexed with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins and represents the first evidence that kanadaptin is likely involved in a phosphorylation-mediated signaling pathway. These results will be of use for designing experiments to further probe the function of kanadaptin.
Published: 2014

21. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin

Author: Xu, Qingping, Deller, Marc C, Nielsen, Tine K, Grant, Joanna C, Lesley, Scott A, Elsliger, Marc-André, Deacon, Ashley M, Wilson, Ian A, Xu, Qingping, Deller, Marc C, Nielsen, Tine K, Grant, Joanna C, Lesley, Scott A, Elsliger, Marc-André, Deacon, Ashley M, and Wilson, Ian A
Abstract: Kanadaptin is a nuclear protein of unknown function that is widely expressed in mammalian tissues. The crystal structure of the forkhead-associated (FHA) domain of human kanadaptin was determined to 1.6 Å resolution. The structure reveals an asymmetric dimer in which one monomer is complexed with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins and represents the first evidence that kanadaptin is likely involved in a phosphorylation-mediated signaling pathway. These results will be of use for designing experiments to further probe the function of kanadaptin.
Published: 2014

22. Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

Author: Coggill, Penelope, Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, Bateman, Alex, Coggill, Penelope, Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, and Bateman, Alex
Abstract: BackgroundEvery genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology.ResultsWe analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria.ConclusionsBased on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide.
Published: 2013

23. Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

Author: Coggill, Penelope, Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, Bateman, Alex, Coggill, Penelope, Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, and Bateman, Alex
Abstract: BackgroundEvery genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology.ResultsWe analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria.ConclusionsBased on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide.
Published: 2013

24. Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding

Author: Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA, Joint Center for Structural Genomics, http://www.jcsg.org , USA, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA, Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA, Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA, Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA, Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA, Kumar, Abhinav, Lomize, Andrei, Jin, Kevin K., Carlton, Dennis, Miller, Mitchell D., Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C., Duan, Lian, Feuerhelm, Julie, Grant, Joanna C., Grzechnik, Anna, Han, Gye Won, Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Marciano, David, Mcmullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L., Sefcovic, Natasha, Tien, Henry J., Trame, Christine B., Van Den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-Andr??, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., Wilson, Ian A., Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA, Joint Center for Structural Genomics, http://www.jcsg.org , USA, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA, Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA, Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA, Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA, Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA, Kumar, Abhinav, Lomize, Andrei, Jin, Kevin K., Carlton, Dennis, Miller, Mitchell D., Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Chiu, Hsiu-Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C., Duan, Lian, Feuerhelm, Julie, Grant, Joanna C., Grzechnik, Anna, Han, Gye Won, Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Marciano, David, Mcmullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L., Sefcovic, Natasha, Tien, Henry J., Trame, Christine B., Van Den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-Andr??, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., and Wilson, Ian A.
Abstract: The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica , respectively, have been determined at 1.8 and 2.25???14?? resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the ??/?? SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their ??2 and ??3 helices. In the `open' conformation (YP_001095227.1), these helices are 15???14?? apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their `open' monomeric state by inserting their amphiphilic helices, ??2 and ??3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.
Published: 2011

25. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism.

Author: Chiu, Hsiu Ju, Chiu, Hsiu Ju, Bakolitsa, Constantina, Skerra, Arne, Lomize, Andrei, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Chiu, Hsiu Ju, Chiu, Hsiu Ju, Bakolitsa, Constantina, Skerra, Arne, Lomize, Andrei, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.
Published: 2010

26. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu.

Author: Das, Debanu, Das, Debanu, Finn, Robert D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Finn, Robert D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 Å resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 Å over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.
Published: 2010

27. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Kumar, Abhinav, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Kumar, Abhinav, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.
Published: 2010

28. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

Author: Miller, Mitchell D, Miller, Mitchell D, Aravind, L, Bakolitsa, Constantina, Rife, Christopher L, Carlton, Dennis, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Miller, Mitchell D, Miller, Mitchell D, Aravind, L, Bakolitsa, Constantina, Rife, Christopher L, Carlton, Dennis, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
Published: 2010

29. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Bateman, Alex, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Bateman, Alex, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott, and Wilson, Ian A
Abstract: The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.
Published: 2010

30. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.

Author: Das, Debanu, Das, Debanu, Grishin, Nick V, Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Grishin, Nick V, Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.
Published: 2010

31. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.

Author: Krishna, S Sri, Krishna, S Sri, Aravind, L, Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Krishna, S Sri, Krishna, S Sri, Aravind, L, Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein-protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).
Published: 2010

32. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Xu, Qingping, Rife, Christopher L, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Xu, Qingping, Rife, Christopher L, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.
Published: 2010

33. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.

Author: Axelrod, Herbert L, Axelrod, Herbert L, Kozbial, Piotr, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Zubieta, Chloe, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Axelrod, Herbert L, Axelrod, Herbert L, Kozbial, Piotr, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Zubieta, Chloe, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006), Proteins, 65, 1046-1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.
Published: 2010

34. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.

Author: Han, Gye Won, Han, Gye Won, Bakolitsa, Constantina, Miller, Mitchell D, Kumar, Abhinav, Carlton, Dennis, Najmanovich, Rafael J, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Han, Gye Won, Han, Gye Won, Bakolitsa, Constantina, Miller, Mitchell D, Kumar, Abhinav, Carlton, Dennis, Najmanovich, Rafael J, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.
Published: 2010

35. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.

Author: Das, Debanu, Das, Debanu, Kozbial, Piotr, Han, Gye Won, Carlton, Dennis, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Elsliger, Marc André, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grant, Joanna C, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Kozbial, Piotr, Han, Gye Won, Carlton, Dennis, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Elsliger, Marc André, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grant, Joanna C, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.
Published: 2010

36. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.

Author: Han, Gye Won, Han, Gye Won, Yang, Xiang Lei, McMullan, Daniel, Chong, Yeeting E, Krishna, S Sri, Rife, Christopher L, Weekes, Dana, Brittain, Scott M, Abdubek, Polat, Ambing, Eileen, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, van den Bedem, Henry, White, Aprilfawn, Wolf, Guenter, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Elsliger, Marc André, Schimmel, Paul, Wilson, Ian A, Han, Gye Won, Han, Gye Won, Yang, Xiang Lei, McMullan, Daniel, Chong, Yeeting E, Krishna, S Sri, Rife, Christopher L, Weekes, Dana, Brittain, Scott M, Abdubek, Polat, Ambing, Eileen, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, van den Bedem, Henry, White, Aprilfawn, Wolf, Guenter, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Elsliger, Marc André, Schimmel, Paul, and Wilson, Ian A
Abstract: A novel aminoacyl-tRNA synthetase that contains an iron-sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron-sulfur [4Fe-4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an L-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe-4S] cluster-binding motif (C-x₂₂-C-x₆-C-x₂-C). It is speculated that the iron-sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.
Published: 2010

37. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism.

Author: Chiu, Hsiu Ju, Chiu, Hsiu Ju, Bakolitsa, Constantina, Skerra, Arne, Lomize, Andrei, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Chiu, Hsiu Ju, Chiu, Hsiu Ju, Bakolitsa, Constantina, Skerra, Arne, Lomize, Andrei, Carlton, Dennis, Miller, Mitchell D, Krishna, S Sri, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.
Published: 2010

38. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu.

Author: Das, Debanu, Das, Debanu, Finn, Robert D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Finn, Robert D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Cai, Xiaohui, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Yeh, Andrew, Zhou, Jiadong, Hodgson, Keith O, Wooley, John, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 Å resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 Å over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.
Published: 2010

39. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris.

Author: Axelrod, Herbert L, Axelrod, Herbert L, Kozbial, Piotr, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Zubieta, Chloe, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Axelrod, Herbert L, Axelrod, Herbert L, Kozbial, Piotr, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Tien, Henry J, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Zubieta, Chloe, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006), Proteins, 65, 1046-1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.
Published: 2010

40. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.

Author: Krishna, S Sri, Krishna, S Sri, Aravind, L, Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Krishna, S Sri, Krishna, S Sri, Aravind, L, Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein-protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).
Published: 2010

41. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Bateman, Alex, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Bateman, Alex, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Kumar, Abhinav, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott, and Wilson, Ian A
Abstract: The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.
Published: 2010

42. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Xu, Qingping, Rife, Christopher L, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Xu, Qingping, Rife, Christopher L, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Lam, Winnie W, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.
Published: 2010

43. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.

Author: Das, Debanu, Das, Debanu, Kozbial, Piotr, Han, Gye Won, Carlton, Dennis, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Elsliger, Marc André, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grant, Joanna C, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Kozbial, Piotr, Han, Gye Won, Carlton, Dennis, Jaroszewski, Lukasz, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Elsliger, Marc André, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grant, Joanna C, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.
Published: 2010

44. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

Author: Miller, Mitchell D, Miller, Mitchell D, Aravind, L, Bakolitsa, Constantina, Rife, Christopher L, Carlton, Dennis, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Miller, Mitchell D, Miller, Mitchell D, Aravind, L, Bakolitsa, Constantina, Rife, Christopher L, Carlton, Dennis, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chiu, Hsiu Ju, Clayton, Thomas, Deller, Marc C, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
Published: 2010

45. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.

Author: Han, Gye Won, Han, Gye Won, Yang, Xiang Lei, McMullan, Daniel, Chong, Yeeting E, Krishna, S Sri, Rife, Christopher L, Weekes, Dana, Brittain, Scott M, Abdubek, Polat, Ambing, Eileen, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, van den Bedem, Henry, White, Aprilfawn, Wolf, Guenter, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Elsliger, Marc André, Schimmel, Paul, Wilson, Ian A, Han, Gye Won, Han, Gye Won, Yang, Xiang Lei, McMullan, Daniel, Chong, Yeeting E, Krishna, S Sri, Rife, Christopher L, Weekes, Dana, Brittain, Scott M, Abdubek, Polat, Ambing, Eileen, Astakhova, Tamara, Axelrod, Herbert L, Carlton, Dennis, Caruthers, Jonathan, Chiu, Hsiu Ju, Clayton, Thomas, Duan, Lian, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Slawomir K, Jaroszewski, Lukasz, Jin, Kevin K, Klock, Heath E, Knuth, Mark W, Kumar, Abhinav, Marciano, David, Miller, Mitchell D, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Paulsen, Jessica, Reyes, Ron, van den Bedem, Henry, White, Aprilfawn, Wolf, Guenter, Xu, Qingping, Hodgson, Keith O, Wooley, John, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Elsliger, Marc André, Schimmel, Paul, and Wilson, Ian A
Abstract: A novel aminoacyl-tRNA synthetase that contains an iron-sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron-sulfur [4Fe-4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an L-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe-4S] cluster-binding motif (C-x₂₂-C-x₆-C-x₂-C). It is speculated that the iron-sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.
Published: 2010

46. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.

Author: Bakolitsa, Constantina, Bakolitsa, Constantina, Kumar, Abhinav, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Bakolitsa, Constantina, Bakolitsa, Constantina, Kumar, Abhinav, Jin, Kevin K, McMullan, Daniel, Krishna, S Sri, Miller, Mitchell D, Abdubek, Polat, Acosta, Claire, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Carlton, Dennis, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Elias, Ylva, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Grzechnik, Slawomir K, Han, Gye Won, Jaroszewski, Lukasz, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Marciano, David, Morse, Andrew T, Murphy, Kevin D, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, Trout, Christina V, van den Bedem, Henry, Weekes, Dana, White, Aprilfawn, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.
Published: 2010

47. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.

Author: Das, Debanu, Das, Debanu, Grishin, Nick V, Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Das, Debanu, Das, Debanu, Grishin, Nick V, Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Burra, Prasad, Chen, Connie, Chiu, Hsiu Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C, Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L, Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K, Grant, Joanna C, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.
Published: 2010

48. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.

Author: Han, Gye Won, Han, Gye Won, Bakolitsa, Constantina, Miller, Mitchell D, Kumar, Abhinav, Carlton, Dennis, Najmanovich, Rafael J, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Han, Gye Won, Han, Gye Won, Bakolitsa, Constantina, Miller, Mitchell D, Kumar, Abhinav, Carlton, Dennis, Najmanovich, Rafael J, Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L, Chen, Connie, Chiu, Hsiu Ju, Clayton, Thomas, Das, Debanu, Deller, Marc C, Duan, Lian, Ernst, Dustin, Feuerhelm, Julie, Grant, Joanna C, Grzechnik, Anna, Jaroszewski, Lukasz, Jin, Kevin K, Johnson, Hope A, Klock, Heath E, Knuth, Mark W, Kozbial, Piotr, Krishna, S Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T, Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L, Sefcovic, Natasha, Tien, Henry J, Trame, Christine B, van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O, Wooley, John, Elsliger, Marc André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A
Abstract: The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.
Published: 2010

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Publication Year Range

Publication Type

Database

Publisher

48 results on '"Xu, Qingping"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources