A standard orientation for metallopeptidases

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1824, Issue 1, 2012, Pages 157-163

  Gomis Rüth, F Xavier ^a   Botelho, Tiago O ^a   Bode, Wolfram ^b  

^a INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Active site cleft; Catalytic mechanism; Catalytic metal ion; Metallopeptidases; Three dimensional structure; Visualization

Indexed keywords

BACTERIAL ENZYME; CARBOXYPEPTIDASE; CARBOXYPEPTIDASE A; CARBOXYPEPTIDASE A4; METAL ION; METALLOPROTEINASE; PEPTIDYLLYSINE METALLOENDOPEPTIDASE; PITRILYSIN; PROTEINASE; THERMOLYSIN; ULILYSIN; UNCLASSIFIED DRUG;

BACILLUS; BINDING SITE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; GRIFOLA FRONDOSA; HUMAN; METAL BINDING; METHANOSARCINA; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; STAPHYLOCOCCUS AUREUS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; TRYPANOSOMA CRUZI;

ANIMALS; CELL POLARITY; HUMANS; METALLOPROTEASES; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PHYLOGENY; PROTEIN CONFORMATION; REFERENCE STANDARDS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 82755187274     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2011.04.014     Document Type: Review

References (43)

1. C. de Duve, B.C. Pressman, R. Gianetto, R. Wattiaux, and F. Appelmans Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue Biochem. J. 60 1955 604 617
2. N. Abramowitz, I. Schechter, and A. Berger On the size of the active site in proteases. II. Carboxypeptidase-A. Biochem. Biophys. Res. Commun. 29 1967 862 867
3. I. Schechter, and A. Berger On the size of active site in proteases. I. Papain Biochem. Biophys. Res. Commun. 27 1967 157 162
4. B.W. Matthews Structural basis of the action of thermolysin and related zinc peptidases Acc. Chem. Res. 21 1988 333 340
5. D.S. Auld 68. Catalytic mechanisms for metallopeptidases A.J. Barrett, N.D. Rawlings, J.F. Woessner Jr. Handbook of proteolytic enzymes vol. 1 2004 Elsevier Academic Press London 268 289
6. A. Bayés, D. Fernández, M. Solà, A. Marrero, S. García-Piqué, F.X. Avilés, J. Vendrell, and F.X. Gomis-Rüth Caught after the Act: a human A-type metallocarboxypeptidase in a product complex with a cleaved hexapeptide Biochemistry 46 2007 6921 6930
7. F.X. Gomis-Rüth Structure and mechanism of metallocarboxypeptidases Crit. Rev. Biochem. Mol. Biol. 43 2008 319 345
8. N.D. Rawlings, A.J. Barrett, and A. Bateman MEROPS: the peptidase database Nucleic Acids Res. 38 2010 D227 D233
9. A.P. Lewis, and P.J. Thomas A novel clan of zinc metallopeptidases with possible intramembrane cleavage properties Protein Sci. 8 1999 439 442 (Pubitemid 29072446)
10. N.M. Hooper Families of zinc metalloproteases FEBS Lett. 354 1994 1 6 (Pubitemid 24331694)
11. W. Jiang, and J.S. Bond Families of metalloendopeptidases and their relationships FEBS Lett. 312 1992 110 114
12. K. Maskos, and W. Bode Structural basis of matrix metalloproteinases and tissue inhibitors of metalloproteinases Mol. Biotechnol. 25 2003 241 266 (Pubitemid 37410016)
13. F.X. Gomis-Rüth Structural aspects of the metzincin clan of metalloendopeptidases Mol. Biotechnol. 24 2003 157 202 (Pubitemid 36623584)
14. F.X. Gomis-Rüth Catalytic domain architecture of metzincin metalloproteases J. Biol. Chem. 284 2009 15353 15357
15. W. Bode, F.X. Gomis-Rüth, and W. Stöcker 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 1993 134 140 (Pubitemid 23285641)
16. W. Stöcker, F. Grams, U. Baumann, P. Reinemer, F.X. Gomis-Rüth, D.B. McKay, and W. Bode The metzincins-topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases Protein Sci. 4 1995 823 840
17. J.H. McKerrow Human fibroblast collagenase contains an amino acid sequence homologous to the zinc-binding site of Serratia protease J. Biol. Chem. 262 1987 5943-5943
18. P.K. Madala, J.D.A. Tyndall, T. Nall, and D.P. Fairlie Update 1 of: Proteases universally recognize beta strands In their active sites Chem. Rev. 110 2010 PR1 PR31
19. M.T. Stubbs, and W. Bode A player of many parts: the spotlight falls on thrombin's structure Thromb. Res. 69 1993 1 58 (Pubitemid 23068230)
20. B.W. Matthews, J.N. Jansonius, P.M. Colman, B.P. Schoenborn, and D. Dupourque Three-dimensional structure of thermolysin Nature 238 1972 37 41
21. B.W. Matthews, L.H. Weaver, and W.R. Kester The conformation of thermolysin J. Biol. Chem. 249 1974 8030 8044
22. M.A. Holmes, and B.W. Matthews Structure of thermolysin refined at 1.6 Å resolution J. Mol. Biol. 160 1982 623 639 (Pubitemid 13244372)
23. G.N. Reeke, J.A. Hartsuck, M.L. Ludwig, F.A. Quiocho, T.A. Steitz, and W.N. Lipscomb The structure of carboxypeptidase A. VI. Some results at 2.0-Å resolution, and the complex with glycyl-tyrosine at 2.8-Å resolution. Proc. Natl. Acad. Sci. USA 58 1967 2220 2226
24. W. Bode, F.X. Gomis-Rüth, R. Huber, R. Zwilling, and W. Stöcker Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases Nature 358 1992 164 167
25. H.M. Holden, D.E. Tronrud, A.F. Monzingo, L.H. Weaver, and B.W. Matthews Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues Biochemistry 26 1987 8542 8553
26. S. Waltersperger, C. Widmer, M. Wang, and U. Baumann Crystal structure of archaemetzincin AmzA from Methanopyrus kandleri at 1.5 Å resolution. Proteins 78 2010 2720 2723
27. T. Goulas, J.L. Arolas, and F.X. Gomis-Rüth Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog Proc. Natl. Acad. Sci. USA 108 2010 1856 1861
28. C. Tallant, R. García-Castellanos, U. Baumann, and F.X. Gomis-Rüth On the relevance of the Met-turn methionine in metzincins J. Biol. Chem. 285 2010 13951 13957
29. T. Hori, T. Kumasaka, M. Yamamoto, N. Nonaka, N. Tanaka, Y. Hashimoto, U. Ueki, and K. Takio Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms Acta Crystallogr., Sect. D 57 2001 361 368 (Pubitemid 32203169)
30. L. Feng, H. Yan, Z. Wu, N. Yan, Z. Wang, P.D. Jeffrey, and Y. Shi Structure of a site-2 protease family intramembrane metalloprotease Science 318 2007 1608 1612 (Pubitemid 350233656)
31. K. Maskos Pitrilysins/inverzincins A. Messerschmidt, W. Bode, M. Cygler, Handbook of metalloproteins vol. 3 2004 John Wiley & Sons, Ltd. Chichester (UK) 190 198
32. 2, a bacterial enzyme with applications in cancer therapy Structure 5 1997 337 347 (Pubitemid 27169935)
33. K. Håkansson, and C.G. Miller Structure of peptidase T from Salmonella typhimurium Eur. J. Biochem. 269 2002 443 450 (Pubitemid 34128001)
34. J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein Chem. 34 1981 167 339
35. D.L. Ollis, E. Cheah, M. Cygler, B. Dijkstra, F. Frolow, S.M. Franken, M. Harel, S.J. Remington, I. Silman, J. Schrag, J.L. Sussman, K.H.G. Verschueren, and A. Goldman The α/β hydrolase fold Protein Eng. 5 1992 197 211
36. X.S. Puente, and C. López-Otín The PLEES-proteins-a family of structurally related enzymes widely distributed from bacteria to humans Biochem. J. 332 1997 947 949
37. A. Biagini, and A. Puigserver Sequence analysis of the aminoacylase-1 family. A new proposed signature for metalloexopeptidases Comp. Biochem. Physiol. B: Biochem. Mol. Biol. 128 2001 469 481 (Pubitemid 32206552)
38. J.L. Arolas, J. Vendrell, F.X. Aviles, and L.D. Fricker Metallocarboxypeptidases: emerging drug targets in biomedicine Curr. Pharm. Des. 13 2007 349 366 (Pubitemid 46477758)
39. F. Grams, M. Crimmin, L. Hinnes, P. Huxley, M. Pieper, H. Tschesche, and W. Bode Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor Biochemistry 34 1995 14012 14020
40. F. Grams, P. Reinemer, J.C. Powers, T. Kleine, M. Pieper, H. Tschesche, R. Huber, and W. Bode X-ray structures of human neutrophil collagenase complexed with peptide thiol inhibitors. Implications for substrate binding and rational drug design Eur. J. Biochem. 228 1995 830 841
41. C. Tallant, R. García-Castellanos, J. Seco, U. Baumann, and F.X. Gomis-Rüth Molecular analysis of ulilysin, the structural prototype of a new family of metzincin metalloproteases J. Biol. Chem. 281 2006 17920 17928 (Pubitemid 44035591)
42. G. Niemirowicz, and J.J. Cazzulo Changing the substrate specificities of M32 peptidases of T. cruzi by site-directed mutagenesis XLIII. Annual Congress of the Argentinian Society for Research in Biochemical and Molecular Biology (SAIB); 17-20.11.2007., Mar del Plata (Argentina) 2007
43. T.O. Botelho, T. Guevara, A. Marrero, P. Arêde, V.S. Fluxà, J.L. Reymond, D.C. Oliveira, F.X. Gomis-Rüth, Structural and functional analyses reveal that Staphylococcus aureus antibiotic resistance factor HmrA is an endopeptidase, J. Biol. Chem. 286 (in press).