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Your search keyword '"Murphy, Kevin D"' showing total 6 results
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6 results on '"Murphy, Kevin D"'

1. 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, 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

Subjects
Genetics, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Amino Acid Sequence, Bacterial Proteins, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Rhodobacteraceae, Sequence Alignment, Zinc Fingers, Chemical Sciences, Biological Sciences, Biophysics
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

2. 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, 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

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Amino Acid Sequence, Amino Acids, Bacillus, Bordetella bronchiseptica, Chorismate Mutase, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Rhodobacteraceae, Structural Homology, Protein, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
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

3. 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, 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

Subjects
1.1 Normal biological development and functioning, Underpinning research, Amino Acid Sequence, Bacterial Proteins, Catalytic Domain, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Interaction Domains and Motifs, Sequence Alignment, Structural Homology, Protein, Xanthomonas campestris, Zinc Acetate, Chemical Sciences, Biological Sciences, Biophysics
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

4. 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, 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

Subjects
Xanthomonas campestris, Zinc Acetate, Bacterial Proteins, Crystallography, X-Ray, Sequence Alignment, Amino Acid Sequence, Catalytic Domain, Conserved Sequence, Structural Homology, Protein, Models, Molecular, Molecular Sequence Data, Protein Interaction Domains and Motifs, Crystallography, X-Ray, Models, Molecular, Structural Homology, Protein, Biophysics, Chemical Sciences, Biological Sciences
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

5. 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, 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

Subjects
Rhodobacteraceae, Bacterial Proteins, Crystallography, X-Ray, Sequence Alignment, Amino Acid Sequence, Protein Structure, Quaternary, Zinc Fingers, Protein Structure, Tertiary, Models, Molecular, Molecular Sequence Data, Crystallography, X-Ray, Models, Molecular, Protein Structure, Quaternary, Tertiary, Biophysics, Chemical Sciences, Biological Sciences
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

6. 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, 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

Subjects
Bacillus, Bordetella bronchiseptica, Rhodobacteraceae, Chorismate Mutase, Amino Acids, Crystallography, X-Ray, Amino Acid Sequence, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Protein Folding, Models, Molecular, Molecular Sequence Data, Crystallography, X-Ray, Models, Molecular, Protein Structure, Quaternary, Tertiary, Structural Homology, Protein, Biophysics, Chemical Sciences, Biological Sciences
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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