The uncharged surface features surrounding the active site of Escherichia coli DsbA are conserved and are implicated in peptide binding
dc.contributor.author | Guddat, Luke W. | en_US |
dc.contributor.author | Martin, Jennifer L. | en_US |
dc.contributor.author | Bardwell, James C.A. | en_US |
dc.contributor.author | Zander, Thomas | en_US |
dc.date.accessioned | 2015-09-01T19:30:28Z | |
dc.date.available | 2015-09-01T19:30:28Z | |
dc.date.issued | 1997-06 | en_US |
dc.identifier.citation | Guddat, Luke W.; Martin, Jennifer L.; Bardwell, James C.A.; Zander, Thomas (1997). "The uncharged surface features surrounding the active site of Escherichia coli DsbA are conserved and are implicated in peptide binding." Protein Science 6(6): 1148-1156. | en_US |
dc.identifier.issn | 0961-8368 | en_US |
dc.identifier.issn | 1469-896X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/113129 | |
dc.description.abstract | DsbA is a protein‐folding catalyst from the periplasm of Escherichia coli that interacts with newly translocated polypeptide substrate and catalyzes the formation of disulfide bonds in these secreted proteins. The precise nature of the interaction between DsbA and unfolded substrate is not known. Here, we give a detailed analysis of the DsbA crystal structure, now refined to 1.7 Å, and present a proposal for its interaction with peptide.The crystal structure of DsbA implies flexibility between the thioredoxin and helical domains that may be an important feature for the disulfide transfer reaction. A hinge point for domain motion is identified—the type IV β‐turn Phe 63‐Met 64‐Gly 65‐Gly 66, which connects the two domains.Three unique features on the active site surface of the DsbA molecule—a groove, hydrophobic pocket, and hydrophobic patch—form an extensive uncharged surface surrounding the active‐site disulfide. Residues that contribute to these surface features are shown to be generally conserved in eight DsbA homologues. Furthermore, the residues immediately surrounding the active‐site disulfide are uncharged in all nine DsbA proteins.A model for DsbA‐peptide interaction has been derived from the structure of a human thioredoxin:peptide complex. This shows that peptide could interact with DsbA in a manner similar to that with thioredoxin. The active‐site disulfide and all three surrounding uncharged surface features of DsbA could, in principle, participate in the binding or stabilization of peptide. | en_US |
dc.publisher | Cold Spring Harbor Laboratory Press | en_US |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | protein crystallography | en_US |
dc.subject.other | oxidoreductase | en_US |
dc.subject.other | DsbA | en_US |
dc.subject.other | protein disulfide isomerase | en_US |
dc.subject.other | thioredoxin fold | en_US |
dc.subject.other | peptide interaction | en_US |
dc.title | The uncharged surface features surrounding the active site of Escherichia coli DsbA are conserved and are implicated in peptide binding | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Biological Chemistry | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Biology, University of Michigan, Ann Arbor, Michigan, 48109‐1048 | en_US |
dc.contributor.affiliationother | Centre for Drug Design and Development, University of Queensland, Brisbane, QLD 4072, Australia | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/113129/1/5560060603_ftp.pdf | |
dc.identifier.doi | 10.1002/pro.5560060603 | en_US |
dc.identifier.source | Protein Science | en_US |
dc.identifier.citedreference | Nicholls A, Bharadwaj R, Honig B. 1993. GRASP: Graphical representation and analysis of surface properties. Biophysical J 64: A116. | en_US |
dc.identifier.citedreference | Jeng MF, Holmgren A, Dyson HJ. 1995. Proton sharing between cysteine thiols in Escherichia coli thioredoxin: Implications for the mechanism of protein disulfide reduction. Biochemistry 34: 10101 – 10105. | en_US |
dc.identifier.citedreference | Jones TA, Zou JY, Cowan SW, Kjeldgaard M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47: 110 – 119. | en_US |
dc.identifier.citedreference | Kleywegt GJ, Jones TA. 1996. Good model‐building and refinement practice. Methods Enzymol. Forthcoming. | en_US |
dc.identifier.citedreference | Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946 – 950. | en_US |
dc.identifier.citedreference | Laskowski RA, MacArthur MW, Moss DS, Thornton JM. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283 – 291. | en_US |
dc.identifier.citedreference | Martin JL. 1995. Thioredoxin—A fold for all reasons. Structure 3: 245 – 250. | en_US |
dc.identifier.citedreference | Martin JL, Bardwell JCA, Kuriyan J. 1993a. Crystal structure of the DsbA protein required for disulphide bond formation in vivo. Nature 365: 464 – 468. | en_US |
dc.identifier.citedreference | Martin JL, Waksman G, Bardwell JCA, Beckwith J, Kuriyan J. 1993b. Crystallization of DsbA, an Escherichia coli protein required for disulphide bond formation in vivo. J Mol Biol 230: 1097 – 1100. | en_US |
dc.identifier.citedreference | Missiakas D, Georgopoulos C, Raina S. 1993. Identification and characterization of the Escherichia coli gene dsbB, whose product is involved in the formation of disulfide bonds in vivo. Proc Natl Acad Sci USA 90: 7084 – 7088. | en_US |
dc.identifier.citedreference | Nakai K, Kanehisa M. 1991. Expert system for predicting protein localization sites in Gram‐negative bacteria. Proteins Struct Funct Genet 11: 95 – 110. | en_US |
dc.identifier.citedreference | Ng TCN, Kwik JF, Maier RJ. 1996. Cloning and expression of the gene for a protein disulfide oxidoreductase from Azotobacter vinelandii: Complementation of an E. coli dsba mutant strain. Gene. Forthcoming. | en_US |
dc.identifier.citedreference | Peek JA, Taylor RK. 1992. Characterization of a periplasmic thiol:disulfide interchange protein required for the functional maturation of secreted virulence factors of Vibrio cholerae. Proc Natl Acad Sci USA 89: 6210 – 6214. | en_US |
dc.identifier.citedreference | Qin J, Clore GM, Gronenborn AM. 1996a. Ionization equilibria for side‐chain carboxyl groups in oxidized and reduced human thioredoxin and in the complex with its target peptide from the transcription factor NF K B. Biochemistry 35: 7 – 13. | en_US |
dc.identifier.citedreference | Qin J, Clore GM, Kennedy WP, Kuszewski J, Gronenborn AM. 1996b. The solution structure of human thioredoxin complexed with its target from Ref‐l reveals peptide chain reversal. Structure 4: 613 – 620. | en_US |
dc.identifier.citedreference | Shevchik VE, Bortoli‐German I, Robert‐Baudouy J, Robinet S, Barras F, Condemine G. 1995. Differential effect of dsbA and dsbC mutations on extracellular enzyme secretion in Erwinia chrysanthemi. Mol Microbiol 16: 745 – 753. | en_US |
dc.identifier.citedreference | Stanfield RL, Takimoto‐Kamimura M, Rini JM, Profy AT, Wilson IA. 1993. Major antigen‐induced domain rearrangements in an antibody. Structure 1: 83 – 93. | en_US |
dc.identifier.citedreference | Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673 – 4680. | en_US |
dc.identifier.citedreference | Tomb JF. 1992. A periplasmic protein disulfide oxidoreductase is required for transformation of Haemophilus influenzae Rd. Proc Natl Acad Sci USA 89: 10252 – 10256. | en_US |
dc.identifier.citedreference | Watarai M, Tobe T, Yoshikawa M, Sasakawa C. 1995. Disulfide oxidoreductase activity of Shigella flexneri is required for release of Ipa proteins and invasion of epithelial cells. Proc Natl Acad Sci USA 92: 4927 – 4931. | en_US |
dc.identifier.citedreference | Wunderlich M, Glockshuber R. 1993a. In vivo control of redox potential during protein folding catalyzed by bacterial protein disulfide isomerase (DsbA). J Biol Chem 268: 24547 – 24550. | en_US |
dc.identifier.citedreference | Wunderlich M, Glockshuber R. 1993b. Redox properties of protein disulfide isomerase (DsbA) from Escherichia coli. Protein Sci 2: 717 – 726. | en_US |
dc.identifier.citedreference | Wunderlich M, Otto A, Seckler R, Glockshuber R. 1993. Bacterial protein disulfide isomerase (DsbA): Efficient catalysis of oxidative protein folding at acidic pH. Biochemistry 32: 12251 – 12256. | en_US |
dc.identifier.citedreference | Yu J, Webb H, Hurst TR. 1992. A homologue of the Escherichia coli DsbA protein involved in disulphide bond formation is required for the enterotoxin biogenesis in Vibrio cholerae. Mol Microbiol 6: 1949 – 1958. | en_US |
dc.identifier.citedreference | Zapun A, Cooper L, Creighton TE. 1994. Replacement of the active‐site cysteine residues of DsbA, a protein required for disulfide bond formation in vivo. Biochemistry 33: 1907 – 1914. | en_US |
dc.identifier.citedreference | Zapun A, Creighton TE. 1994. Effects of DsbA on the disulfide folding of bovine pancreatic trypsin inhibitor and α–lactalbumin. Biochemistry 33: 5202 – 5211. | en_US |
dc.identifier.citedreference | Bardwell JCA. 1994. Building bridges: Disulfide bond formation in the cell. Mol Microbiol 14: 199 – 205. | en_US |
dc.identifier.citedreference | Bardwell JCA, Lee JO, Jander G, Martin N, Belin D, Beckwith J. 1993. A pathway for disulfide bond formation in vivo. Proc Natl Acad Sci USA 90: 1038 – 1042. | en_US |
dc.identifier.citedreference | Bardwell JCA, McGovern K, Beckwith J. 1991. Identification of a protein required for disulfide bond formation in vivo. Cell 67: 581 – 589. | en_US |
dc.identifier.citedreference | Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr., Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer‐based archival file for macromolecular structures. J Mol Biol 112: 535 – 542. | en_US |
dc.identifier.citedreference | Brünger AT. 1992a. Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472 – 475. | en_US |
dc.identifier.citedreference | Brünger AT. 1992b. X‐PLOR (version 3.1) manual. New Haven, Connecticut: Yale University. | en_US |
dc.identifier.citedreference | Darby NJ, Creighton TE. 1995. Catalytic mechanism of DsbA and its comparison with that of protein disulfide isomerase. Biochemistry 34: 3576 – 3587. | en_US |
dc.identifier.citedreference | Engh RA, Huber R. 1991. Accurate bond lengths and angle parameters for X‐ray protein structure refinement. Acta Crystallogr A 47: 392 – 400. | en_US |
dc.identifier.citedreference | Frech C, Wunderlich M, Glockshuber R, Schmid FX. 1996. Preferential binding of unfolded protein to DsbA. EMBO J 15: 392 – 398. | en_US |
dc.identifier.citedreference | Freedman RB, Hirst TR, Tuite MF. 1994. Protein disulphide isomerase—Building bridges in protein folding. Trends Biochem Sci 19: 331 – 336. | en_US |
dc.identifier.citedreference | Friedrich MJ, Kinsey NE, Vila J, Kadner RJ. 1993. Nucleotide sequence of a 13.9 kb segment of the 90 kb virulence plasmid of Salmonella typhimurium: The presence of fimbral biosynthetic genes. Mol Microbiol 8: 543 – 558. | en_US |
dc.identifier.citedreference | Wilson NA, Barbar E, Fuchs JA, Woodward C. 1995. Aspartic acid 26 in Escherichia coli thioredoxin has a p K a > 9. Biochemistry 34: 8931 – 8939. | en_US |
dc.identifier.citedreference | Guilhot C, Jander G, Martin NL, Beckwith J. 1995. Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA. Proc Nutl Acad Sci USA 92: 9895 – 9899. | en_US |
dc.identifier.citedreference | Herron JN, He XM, Ballard DW, Blier PR, Pace PE, Bothwell ALM, Voss EW Jr., Edmundson AB. 1991. An autoantibody to single‐stranded DNA: Comparison of the three‐dimensional structures of the unliganded Fab and a deoxynucleotide‐Fab complex. Proteins Struct Funct Genet 11: 159 – 175. | en_US |
dc.identifier.citedreference | Higashi T. 1990. R‐AXIS‐IIC, a program for indexing and processing R‐AXIS IIC imaging plate data. Danvers, Massachusetts: Rigaku. | en_US |
dc.identifier.citedreference | Hu SH, Peek JA, Rattigan E, Taylor RK, Martin JL. 1997. Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae. J Mol Biol 268: 137 – 146. | en_US |
dc.identifier.citedreference | Huber R, Epp O, Steigemann W, Formanek H. 1971. The atomic structure of erythrocruorin in the light of the chemical sequence and its comparison with myoglobin. Eur J Biochem 19: 42 – 50. | en_US |
dc.identifier.citedreference | Hutchinson EG, Thornton JM. 1996. PROMOTIF—A program to identify and analyze structural motifs in proteins. Protein Sci 5: 212 – 220. | en_US |
dc.identifier.citedreference | Jander G, Martin NL, Beckwith J. 1994. Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation. EMBO J 13: 5121 – 5127. | en_US |
dc.identifier.citedreference | Jeng MF, Dyson HJ. 1996. Direct measurement of the aspartic acid 26 p K a for reduced Escherichia coli thioredoxin by 13C NMR. Biochemistry 35: 1 – 6. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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