Probing the role of divalent metal ions in a bacterial psychrophilic metalloprotease: Binding studies of an enzyme in the crystalline state by X-ray crystallography

Journal of Bacteriology

Volumn 185, Issue 14, 2003, Pages 4195-4203

  Ravaud, Stephanie ^a   Gouet, Patrice ^a   Haser, Richard ^a   Aghajari, Nushin ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALKALINE PROTEINASE; CALCIUM ION; DIVALENT CATION; EDETIC ACID; METAL ION; METALLOPROTEINASE; ZINC;

AMINO ACID METABOLISM; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BACTERIAL MEMBRANE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; COLD ACCLIMATIZATION; CRYSTALLIZATION; ENZYME ACTIVE SITE; ENZYME BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; RESIDUE ANALYSIS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CALCIUM; CATIONS, DIVALENT; COLD; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; METALLOENDOPEPTIDASES; MODELS, MOLECULAR; PROTEIN BINDING; PSEUDOMONAS; ZINC;

ANIMALIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; PSEUDOMONAS;

EID: 0038492504     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.14.4195-4203.2003     Document Type: Article

References (31)

1. Aghajari, N., F. Van Petegem, V. Villeret, J. P. Chessa, C. Gerday, R. Haser, and J. Van Beeumen. 2003. Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases. Proteins Struct. Funct. Genet. 50:636-647.
2. Baumann, U. 1994. Crystal structure of the 50-kDa metalloprotease from Serratia marcescens. J. Mol. Biol. 242:244-251.
3. Baumann, U., S. Wu, K. M. Flaherty, and D. B. McKay. 1993. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12:3357-3364.
4. Bode, W., F. X. Gomis-Ruth, R. Huber, R. Zwilling, and W. Stocker. 1992. Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases. Nature 358:164-167.
5. Bode, W., F. X. Gomis-Ruth, and W. Stockler. 1993. Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HEXXHXXGXXH and Met-turn) and topologies and should be grouped into a common family, the "metzincins." FEBS Lett. 331:134-140.
6. Bode, W., P. Reinemer, R. Huber, T. Kleine, S. Schnierer, and H. Tschesche. 1994. The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity. EMBO J. 13:1263-1269.
7. Borkakoti, N., F. K. Winkler, D. H. Williams, A. D'Arcy, M. J. Broadhurst, P. A. Brown, W. H. Johnson, and E. J. Murray. 1994. Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Nat. Struct. Biol. 1:106-110.
8. Brünger, A. T. 1992. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472-475.
9. Brünger, A. T., P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J. S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, and G. L. Warren. 1998. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D54:905-921.
10. CCP4 Collaborative Computational Project. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50:760-763.
11. Chessa, J. P., I. Petrescu, M. Bentahir, J. Van Beeumen, and C. Gerday. 2000. Purification, physico-chemical characterization and sequence of a heat labile alkaline metalloprotease isolated from a psychrophilic Pseudomonas species. Biochim. Biophys. Acta 1479:265-274.
12. Delepelaire, P. 1994. PrtD, the integral membrane ATP-binding cassette component of the Erwinia chrysanthemi metalloprotease secretion system, exhibits a secretion signal-regulated ATPase activity. J. Biol. Chem. 269:27952-27957.
13. Delepelaire, P., and C. Wandersman. 1989. Protease secretion by Erwinia chrysanthemi: proteases B and C are synthesized and secreted as zymogens without a signal peptide. J. Biol. Chem. 264:9083-9089.
14. Delepelaire, P., and C. Wandersman. 1990. Protein secretion in gram-negative bacteria. The extracellular metalloprotease B from Erwinia chrysanthemi contains a C-terminal secretion signal analogous to that of Escherichia coli alpha-hemolysin. J. Biol. Chem. 265:17118-17125.
15. Dive, V., M. Kaczorek, C. Roussel, and F. Roux. 1997. Les nouveaux inhibiteurs des métalloprotéinases à zinc. Biofutur 167:29-33.
16. Feller, G., and C. Gerday. 1997. Psychrophilic enzymes: molecular basis of cold adaptation. Cell. Mol. Life Sci. 53:830-841.
17. Feller, G., E. Narinx, J. L. Arpigny, M. Aittaleb, E. Baise, S. Genicots, and C. Gerday. 1996. Enzymes from psychrophilic organisms. FEMS Microbiol. Rev. 18:189-202.
18. Gerday, C., M. Aittaleb, J. L. Arpigny, E. Baise, J. P. Chessa, G. Garsoux, I. Petrescu, and G. Feller. 1997. Psychrophilic enzymes: a thermodynamic challenge. Biochim. Biophys. Acta 1342:119-131.
19. Gomis-Ruth, F. X., L. F. Kress, and W. Bode. 1993. First structure of a snake venom metalloproteinase: a prototype for matrix metalloproteinases/collagenases. EMBO J. 12:4151-4157.
20. Gomis-Ruth, F. X., L. F. Kress, J. Kellermann, I. Mayr, X. Lee, R. Huber, and W. Bode. 1994. Refined 2.0 Å X-ray crystal structure of the snake venom zinc-endopeptidase adamalysin II: primary and tertiary structure determination, refinement, molecular structure, and comparison with astacin, collagenase and thermolysin. J. Mol. Biol. 239:513-544.
21. Gomis-Ruth, F. X., W. Stocker, R. Huber, R. Zwilling, and W. Bode. 1993. Refined 1.8 Å X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L.: structure determination, refinement, molecular structure, and comparison with thermolysin. J. Mol. Biol. 229:945-968.
22. Hooft, R. W., G. Vriend, C. Sander, and E. E. Abola. 1996. Errors in protein structures. Nature 381:272.
23. Kabsch, W. 1993. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26:795-800.
24. Laskowski, R. A., M. W. MacArthur, and D. S. Moss. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
25. Leslie, A. G. W. 1991. Molecular data processing, p. 50-61. In D. Moras, A. D. Podjarny, and J. C. Thierry (ed.), Crystallography computing. Oxford University Press, Oxford, United Kingdom.
26. Navaza, J. 2001. Implementation of molecular replacement in AMoRe. Acta Crystallogr. D57:1367-1372.
27. Otwinoswki, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326
28. Rose, T., P. Sebo, J. Bellalou, and D. Ladant. 1995. Interaction of calcium with Bordetella pertussis adenylate cyclase toxin: characterization of multiple calcium-binding sites and calcium-induced conformational changes. J. Biol. Chem. 270:26370-26376.
29. Roussel, A., and C. Cambillau. 1992. TURBO-FRODO. Biographics AFMB, Marseille, France.
30. Russell, N. J. 1998. Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications. Adv. Biochem. Eng. Biotechnol. 61:1-21.
31. Villeret, V., J. P. Chessa, C. Gerday, and J. Van Beeumen. 1997. Preliminary crystal structure determination of the alkaline protease from the Antarctic psychrophile Pseudomonas aeruginosa. Protein Sci. 6:2462-2464.