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Start Over Author "Chen, Connie" Journal acta crystallographica section f structural biology and crystallization communications
21 results on '"Chen, Connie"'

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

Author

Bakolitsa, Constantina, primary, Xu, Qingping, additional, Rife, Christopher L., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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2. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

Author

Axelrod, Herbert L., primary, Das, Debanu, additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Bakolitsa, Constantina, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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3. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 fromExiguobacterium sibiricum255-15

Author

Han, Gye Won, primary, Elsliger, Marc-André, additional, Yeates, Todd O., additional, Xu, Qingping, additional, Murzin, Alexey G., additional, Krishna, S. Sri, additional, Jaroszewski, Lukasz, additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ernst, Dustin, additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Okach, Linda, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Hodgson, Keith O., additional, Wooley, John, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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4. Structure ofBacteroides thetaiotaomicronBT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism

Author

Yeh, Andrew P., primary, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Cai, Xiaohui, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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5. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiontBacteroides thetaiotaomicron

Author

Xu, Qingping, primary, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Cai, Xiaohui, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Yeh, Andrew, additional, Zhou, Jiadong, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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6. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC fromBacillus cereusin complex withL-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

Author

Xu, Qingping, primary, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Cai, Xiaohui, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Yeh, Andrew, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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7. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) fromBacteroides thetaiotaomicronat 2.2 Å resolution

Author

Xu, Qingping, primary, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Cai, Xiaohui, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Yeh, Andrew, additional, Zhou, Jiadong, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-Andre, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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8. 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, primary, Bakolitsa, Constantina, additional, Miller, Mitchell D., additional, Kumar, Abhinav, additional, Carlton, Dennis, additional, Najmanovich, Rafael J., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ernst, Dustin, additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Marciano, David, additional, McMullan, Daniel, additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Okach, Linda, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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9. The structure of BVU2987 fromBacteroides vulgatusreveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Author

Das, Debanu, primary, Finn, Robert D., additional, Carlton, Dennis, additional, Miller, Mitchell D., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Marciano, David, additional, McMullan, Daniel, additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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10. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of theBacilluschorismate mutase fold and suggest a role in amino-acid metabolism

Author

Bakolitsa, Constantina, primary, Kumar, Abhinav, additional, Jin, Kevin K., additional, McMullan, Daniel, additional, Krishna, S. Sri, additional, Miller, Mitchell D., additional, Abdubek, Polat, additional, Acosta, Claire, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Burra, Prasad, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Elias, Ylva, additional, Ellrott, Kyle, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Grzechnik, Slawomir K., additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Marciano, David, additional, Morse, Andrew T., additional, Murphy, Kevin D., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, Trout, Christina V., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, White, Aprilfawn, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-Andre, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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11. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Author

Das, Debanu, primary, Grishin, Nick V., additional, Kumar, Abhinav, additional, Carlton, Dennis, additional, Bakolitsa, Constantina, additional, Miller, Mitchell D., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Burra, Prasad, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grzechnik, Anna, additional, Grzechnik, Slawomir K., additional, Grant, Joanna C., additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Marciano, David, additional, McMullan, Daniel, additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Oommachen, Silvya, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2009
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12. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein fromKlebsiella pneumoniae, reveals an OB-fold

Author

Das, Debanu, primary, Kozbial, Piotr, additional, Han, Gye Won, additional, Carlton, Dennis, additional, Jaroszewski, Lukasz, additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Elsliger, Marc-André, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grzechnik, Anna, additional, Grant, Joanna C., additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Oommachen, Silvya, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2009
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13. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.

Author

Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Cysteine Proteases genetics, Cysteine Proteases metabolism, Endopeptidases genetics, Endopeptidases metabolism, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Substrate Specificity, Bacillus cereus enzymology, Cysteine Proteases chemistry, Endopeptidases chemistry
Abstract

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.

Published
2010
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14. 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 Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacteroides genetics, Crystallography, X-Ray, Fimbriae Proteins genetics, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Bacteroides chemistry, Fimbriae Proteins chemistry, Fimbriae, Bacterial chemistry, Protein Folding
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
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15. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

Author

Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Bacillales enzymology, Pyrophosphatases chemistry
Abstract

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.

Published
2010
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16. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.

Author

Das D, Finn RD, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacteroides metabolism, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Periplasmic Proteins metabolism, Protein Binding, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Bacteroides chemistry, Periplasmic Proteins chemistry
Abstract

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.

Published
2010
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17. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.

Author

Das D, Grishin NV, Kumar A, Carlton D, Bakolitsa C, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Burra P, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Neisseria gonorrhoeae genetics, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Bacterial Proteins chemistry, Gene Expression Regulation, Neisseria gonorrhoeae chemistry, Transcription, Genetic
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
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18. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.

Author

Das D, Kozbial P, Han GW, Carlton D, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Elsliger MA, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grant JC, Jin KK, Johnson HA, Klock HE, Knuth MW, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Bacterial Proteins chemistry, Klebsiella pneumoniae chemistry, Lipoproteins chemistry
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
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19. Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.

Author

Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins metabolism, Bacteroides metabolism, Binding Sites, Carbohydrates chemistry, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Bacterial Proteins chemistry, Bacteroides chemistry, Carbohydrate Metabolism
Abstract

BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.

Published
2010
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20. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.

Author

Xu Q, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Cai X, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Lam WW, Marciano D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Yeh A, Zhou J, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Alignment, Structural Homology, Protein, Bacterial Proteins chemistry, Bacteroides chemistry, Perforin chemistry
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
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21. 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 C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacillus enzymology, Chorismate Mutase metabolism, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Amino Acids metabolism, Bordetella bronchiseptica enzymology, Chorismate Mutase chemistry, Protein Folding, Rhodobacteraceae enzymology
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
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