A large and accurate collection of peptidase cleavages in the MEROPS database

Database

Volumn 2009, Issue , 2009, Pages

  Rawlings, Neil D ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79951810546     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bap015     Document Type: Article

References (58)

1. Emanuelsson, O., Brunak, S., von Heijne, G. et al. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2, 953-971.
2. Weissman, A.M. (1997) Regulating protein degradation by ubiquitination. Immunol. Today, 18, 189-198.
3. Drag, M. and Salvesen, G.S. (2008) DeSUMOylating enzymes-SENPs. IUBMB Life, 60, 734-742.
4. Shen, L.N., Liu, H., Dong, C. et al. (2005) Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1. EMBO J., 24, 1341-1351.
5. Rholam, M. and Fahy, C. (2009) Processing of peptide and hormone precursors at the dibasic cleavage sites. Cell Mol. Life Sci., 66, 2075-2091.
6. Kitabgi, P. (2006) Inactivation of neurotensin and neuromedin N by Zn metallopeptidases. Peptides, 27, 2515-2522.
7. Ghosh, A.K., Gemma, S. and Tang, J. (2008) beta-Secretase as a therapeutic target for Alzheimer's disease. Neurotherapeutics, 5, 399-408.
8. Murphy, G. and Nagase, H. (2008) Reappraising metalloproteinases in rheumatoid arthritis and osteoarthritis: destruction or repair? Nat. Clin. Pract. Rheumatol., 4, 128-135.
9. Churg, A. and Wright, J.L. (2005) Proteases and emphysema. Curr. Opin. Pulm. Med., 11, 153-159.
10. Seiki, M. (2003) Membrane-type 1 matrix metalloproteinase: a key enzyme for tumor invasion. Cancer Lett., 194, 1-11.
11. O'Reilly, D.A., Yang, B.M., Creighton, J.E. et al. (2001) Mutations of the cationic trypsinogen gene in hereditary and non-hereditary pancreatitis. Digestion, 64, 54-60.
12. Ersmark, K., Samuelsson, B. and Hallberg, A. (2006) Plasmepsins as potential targets for new antimalarial therapy. Med. Res. Rev., 26, 626-666.
13. Johansen, J.T. and Ottesen, M. (1968) The proteolytic degradation of the B-chain of oxidized insulin by papain, chymopapain and papaya peptidase. CR Trav. Lab. Carlsberg, 36, 265-283.
14. Schechter, I. and Berger, A. (1968) On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain. Biochem. Biophys. Res. Commun., 32, 898-902.
15. Rodriguez, J., Gupta, N., Smith, R.D. et al. (2008) Does trypsin cut before proline? J. Proteome Res., 7, 300-305.
16. Thornberry, N.A., Chapman, K.T. and Nicholson, D.W. (2000) Determination of caspase specificities using a peptide combinatorial library. Methods Enzymol., 322, 100-110.
17. Fontana, A., De Laureto, P.P., Spolaore, B. et al. (2004) Probing protein structure by limited proteolysis. Acta Biochim. Pol., 51, 299-321.
18. Ruzza, P., Quintieri, L., Osler, A. et al. (2006) Fluorescent, internally quenched, peptides for exploring the pH-dependent substrate specificity of cathepsin B. J. Pept. Sci., 12, 455-461.
19. Schilling, O. and Overall, C.M. (2008) Proteome-derived, databasesearchable peptide libraries for identifying protease cleavage sites. Nat. Biotechnol., 26, 685-694.
20. Rawlings, N.D. and Barrett, A.J. (1993) Evolutionary families of peptidases. Biochem. J., 290, 205-218.
21. Rawlings, N.D., Morton, F.R., Kok, C.Y. et al. (2008) MEROPS: the peptidase database. Nucleic Acids Res., 36, D320-D325.
22. Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (eds), (1998) Handbook of Proteolytic Enzymes, 1st edn., London, Academic Press.
23. Igarashi, Y., Eroshkin, A., Gramatikova, S. et al. (2007) CutDB: a proteolytic event database. Nucleic Acids Res., 35, D546-D549.
24. Luthi, A.U. and Martin, S.J. (2007) The CASBAH: a searchable database of caspase substrates. Cell Death Differ., 14, 641-650.
25. Wheeler, D.L., Barrett, T., Benson, D.A. et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 36, D13-D21.
26. Apweiler, R., Bairoch, A., Wu, C.H. et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 32, D115-D119.
27. Crooks, G.E., Hon, G., Chandonia, J.M. et al. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
28. Suzek, B.E., Huang, H., McGarvey, P. et al. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics, 23, 1282-1288.
29. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
30. Fu, G., Chumanevich, A.A., Agniswamy, J. et al. (2008) Structural basis for executioner caspase recognition of P5 position in substrates. Apoptosis, 13, 1291-1302.
31. Isaya, G., Kalousek, F. and Rosenberg, L.E. (1992) Amino-terminal octapeptides function as recognition signals for the mitochondrial intermediate peptidase. J. Biol. Chem., 267, 7904-7910.
32. Livingstone, C.D. and Barton, G.J. (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
33. Dando, P.M., Fortunato, M., Smith, L. et al. (1999) Pig kidney legumain: an asparaginyl endopeptidase with restricted specificity. Biochem. J., 339, 743-749.
34. Brindley, P.J., Kalinna, B.H., Wong, J.Y.M. et al. (2001) Proteolysis of human hemoglobin by schistosome cathepsin D. Mol. Biochem. Parasitol., 112, 103-112.
35. Kay, J. and Tatnell, P.J. (2004) In Cathepsin, E., Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (eds), Handbook of Proteolytic Enzymes, Elsevier, London, pp. 33-38.
36. Cirman, T., Oresic, K., Mazovec, G.D. et al. (2004) Selective disruption of lysosomes in HeLa cells triggers apoptosis mediated by cleavage of Bid by multiple papain-like lysosomal cathepsins. J. Biol. Chem., 279, 3578-3587.
37. Walle, L.V., Damme, P.V., Lamkanfi, M. et al. (2007) Proteome-wide identification of HtrA2/Omi substrates. J. Proteome Res., 6, 1006-1015.
38. Chan, S.K., Tulloss, I. and Margoliash, E. (1966) Primary structure of the cytochrome c from the snapping turtle, Chelydra serpentina. Biochemistry, 5, 2586-2597.
39. Lorand, L., Jeong, J.M., Radek, J.T. et al. (1993) Human plasma factor XIII: subunit interactions and activation of zymogen. Methods Enzymol., 222, 22-35.
40. Furuta, M., Carroll, R., Martin, S. et al. (1998) Incomplete processing of proinsulin to insulin accompanied by elevation of Des-31, 32 proinsulin intermediates in islets of mice lacking active PC2. J.Biol. Chem., 273, 3431-3437.
41. Scott, P.G. and Pearson, H. (1981) Cathepsin D: specificity of peptidebond cleavage in type-I collagen and effects on type-III collagen and procollagen. Eur. J. Biochem., 114, 59-62.
42. Aimes, R.T. and Quigley, J.P. (1995) Matrix metalloproteinase-2 is an interstitial collagenase. Inhibitor-free enzyme catalyzes the cleavage of collagen fibrils and soluble native type I collagen generating the specific 3/4- and 1/4-length fragments. J. Biol. Chem., 270, 5872-5876.
43. Siegfried, G., Khatib, A.M., Benjannet, S. et al. (2003) The proteolytic processing of pro-platelet-derived growth factor-A at RRKR(86) by members of the proprotein convertase family is functionally correlated to platelet-derived growth factor-A-induced functions and tumorigenicity. Cancer Res., 63, 1458-1463.
44. Borgono, C.A., Michael, I.P., Shaw, J.L. et al. (2007) Expression and functional characterization of the cancer-related serine protease, human tissue kallikrein 14. J. Biol. Chem., 282, 2405-2422.
45. Uhland, K. (2006) Matriptase and its putative role in cancer. Cell Mol. Life Sci., 63, 2968-2978.
46. Karasawa, K., Kudo, I., Kobayashi, T. et al. (1991) Lysophospholipase L1 from Escherichia coli K-12 overproducer. J. Biochem., 109, 288-293.
47. Link, A.J., Robison, K. and Church, G.M. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis, 18, 1259-1313.
48. Shibata, H., Hara, S. and Ikenaka, T. (1988) Amino acid sequence of winged bean (Psophocarpus tetragonolobus (L.) DC.) chymotrypsin inhibitor, WCI-3. J. Biochem., 104, 537-543.
49. Zybailov, B., Rutschow, H., Friso, G. et al. (2008) Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE, 3, e1994.
50. Kimura, J., Arndt, E. and Kimura, M. (1987) Primary structures of three highly acidic ribosomal proteins S6, S12 and S15 from the archaebacterium Halobacterium marismortui. FEBS Lett., 224, 65-70.
51. Shih, M., Lampi, K.J., Shearer, T.R. et al. (1998) Cleavage of beta crystallins during maturation of bovine lens. Mol. Vis., 4, 4.
52. Bae, S.S., Perry, D.K., Oh, Y.S. et al. (2000) Proteolytic cleavage of phospholipase C-gamma1 during apoptosis in Molt-4 cells. FASEB J., 14, 1083-1092.
53. Zhen, E.Y., Brittain, I.J., Laska, D.A. et al. (2008) Characterization of metalloprotease cleavage products of human articular cartilage. Arthritis Rheum., 58, 2420-2431.
54. Menegatti, E., Tedeschi, G., Ronchi, S. et al. (1992) Purification, inhibitory properties and amino acid sequence of a new serine proteinase inhibitor from white mustard (Sinapis alba L.) seed. FEBS Lett., 301, 10-14.
55. Van Damme, P., Maurer-Stroh, S., Plasman, K. et al. (2009) Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol. Cell Proteomics, 8, 258-272.
56. Yanai, K., Takaya, N., Kojima, N. et al. (1992) Purification of two chitinases from Rhizopus oligosporus and isolation and sequencing of the encoding genes. J. Bacteriol., 174, 7398-7406.
57. Dufty, B.M., Warner, L.R., Hou, S.T. et al. (2007) Calpain-cleavage of alpha-synuclein: connecting proteolytic processing to disease-linked aggregation. Am. J. Pathol., 170, 1725-1738.
58. Lamkanfi, M., Kanneganti, T.D., Van Damme, P. et al. (2008) Targeted peptidecentric proteomics reveals caspase-7 as a substrate of the caspase-1 inflammasomes. Mol. Cell Proteomics, 7, 2350-2363.