WORKLIST ENTRIES (1): MICOLLPTASE View alignment Microbial collagenase metalloprotease (M9) signature Type of fingerprint: COMPOUND with 5 elements Links: PRINTS; PR00756 ALADIPTASE; PR00791 PEPDIPTASEA; PR00730 THERMOLYSIN PRINTS; PR00787 NEUTRALPTASE; PR00782 LSHMANOLYSIN; PR00997 FRAGILYSIN PRINTS; PR00786 NEPRILYSIN; PR00765 CRBOXYPTASEA; PR00932 AMINO1PTASE PRINTS; PR00789 OSIALOPTASE; PR00933 BLYTICPTASE; PR00934 XHISDIPTASE PRINTS; PR00919 THERMOPTASE; PR00998 CRBOXYPTASET; PR00768 DEUTEROLYSIN PRINTS; PR00999 FUNGALYSIN; PR01000 SREBPS2PTASE INTERPRO; IPR002169 PROSITE; PS00142 ZINC_PROTEASE PFAM; PF00099 Creation date 09-SEP-1998; UPDATE 07-JUN-1999 1. RAWLINGS, N.D. AND BARRETT, A.J. Evolutionary families of metallopeptidases. METHODS ENZYMOL. 248 183-228 (1995). 2. RAWLINGS, N.D. AND BARRETT, A.J. MEROPS - Peptidase Database http://www.bi.bbsrc.ac.uk/merops/merops.htm 3. RAWLINGS, N.D. AND BARRETT, A.J. Family M9 - Clan MA - Microbial collagenase http://www.bi.bbsrc.ac.uk/merops/famcards/m9.htm 4. BARRETT, A.J., RAWLINGS, N.D. AND WOESSNER, J.F. Vibrio collagenase. IN HANDBOOK OF PROTEOLYTIC ENZYMES, ACADEMIC PRESS, 1998, PP.1096-1098. 5. BARRETT, A.J., RAWLINGS, N.D. AND WOESSNER, J.F. Clostridium collagenases. IN HANDBOOK OF PROTEOLYTIC ENZYMES, ACADEMIC PRESS, 1998, PP.1098-1102. 6. MATSUSHITA, O., YOSHIHARA, K., KATAYAMA, S., MINAMI, J. AND OKABE, A. Purification and characterization of Clostridium perfringens 120-kilodalton collagenase and nucleotide sequence of the corresponding gene. J.BACTERIOL. 176 149-156 (1994). Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date . Of these, around half contain the HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metallo- proteases as abXHEbbHbc, where a is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, b is an uncharged residue, and c a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Metalloproteases can be split into five groups on the basis of their metal- binding residues: the first three contain the HEXXH motif, the other two do not . In the first group, a glutamic acid completes the active site - these are termed HEXXH+E: all families in this group show some sequence relationship and have been assigned to clan MA . The second group, which have a third histidine as the extra metal-binding residue, are termed HEXXH+H and are grouped into clan MB on the basis of their inter-relation- ship. In the third group, the additional metal-binding residues are unidentified. The fourth group is diverse - the metal-binding residues are known but do not form the HEXXH motif. And the fifth group comprises the remaining families where the metal-binding residues are as yet unknown [1,2]. Microbial collagenases have been identified from bacteria of both the Vibrio and Clostridium genuses. They are zinc-containing metallopeptidases that belong to the M25 protease family, which form part of the MA clan [1,3]. Collagenase is used during bacterial attack to degrade the collagen barrier of the host during invasion. Vibrio bacteria are non-pathogenic, and are sometimes used in hospitals to remove dead tissue from burns and ulcers . Clostrium histolyticum is a pathogen that causes gas gangrene; nevertheless, the isolated collagenase has been used to treat bed sores . Collagen cleavage occurs at an Xaa+Gly in Vibrio bacteria and at Yaa+Gly bonds in Clostridium collagenases [4,5]. Analysis of the primary structure of the gene product from Clostridium perfringens has revealed that the enzyme is produced with a stretch of 86 residues that contain a putative signal sequence . Within this stretch is found PLGP, an amino acid sequence typical of collagenase substrates. This sequence may thus be implicated in self-processing of the collagenase . MICOLLPTASE is a 5-element fingerprint that provides a signature for microbial collagenase zinc metallopeptidases (M9). The fingerprint was derived from an initial alignment of 4 sequences: the motifs were drawn from conserved regions spanning virtually the full alignment length - motif 4 includes the region encoded by the PROSITE pattern ZINC_PROTEASE (PS00142), which describes the HEXXH active site; and motif 5 contains the active site glutamate. Two iterations on OWL31.1 were required to reach convergence, at which point a true set comprising 8 sequences was identified. An update on SPTR37_9f identified a true set of 5 sequences, and 1 partial match. SUMMARY INFORMATION 5 codes involving 5 elements 1 codes involving 4 elements 0 codes involving 3 elements 0 codes involving 2 elements COMPOSITE FINGERPRINT INDEX 5| 5 5 5 5 5 4| 0 1 1 1 1 3| 0 0 0 0 0 2| 0 0 0 0 0 --+-------------------------- | 1 2 3 4 5 True positives.. COLA_CLOPE O54108 COLA_VIBAL Q46085 COLA_VIBPA Subfamily: Codes involving 4 elements Subfamily True positives.. O86030 PROTEIN TITLES COLA_CLOPE MICROBIAL COLLAGENASE PRECURSOR (EC 184.108.40.206) (120 KD COLLAG O54108 PUTATIVE SECRETED PROTEASE - STREPTOMYCES COELICOLOR. COLA_VIBAL MICROBIAL COLLAGENASE PRECURSOR (EC 220.127.116.11) - VIBRIO ALGIN Q46085 COLLAGENASE PRECURSOR - CLOSTRIDIUM HISTOLYTICUM. COLA_VIBPA MICROBIAL COLLAGENASE PRECURSOR (EC 18.104.22.168) - VIBRIO PARAH O86030 COLLAGENASE - VIBRIO CHOLERAE.
SCAN HISTORY OWL30_2 1 50 NSINGLE OWL31_1 1 50 NSINGLE SPTR37_9f 2 100 NSINGLE INITIAL MOTIF SETS MICOLLPTASE1 Length of motif = 19 Motif number = 1 Microbial collagenase motif I - 1 PCODE ST INT GIPTLVEFLRAGYYLGFYN COLA_CLOPE 159 159 ELETLFLYLRAGYYAEFYN COLA_VIBAL 144 144 VLENLGEFVRAAYYVRYNA COLA_VIBPA 97 97 RLENYGEFIRAAYYVRYNA AF080248 97 97 MICOLLPTASE2 Length of motif = 15 Motif number = 2 Microbial collagenase motif II - 1 PCODE ST INT LTVVIYNSPEEYKLN COLA_CLOPE 447 269 LQVNIFDSSTDYGKY COLA_VIBAL 415 252 VEVAVFASNDSYVDY COLA_VIBPA 374 258 VEVVVFANNSSYVNY AF080248 374 258 MICOLLPTASE3 Length of motif = 17 Motif number = 3 Microbial collagenase motif III - 1 PCODE ST INT INGFSTDNGGIYIENIG COLA_CLOPE 464 2 IFDISTDNGGMYLEGDP COLA_VIBAL 433 3 LFGNTTDNGGQYLEGTP COLA_VIBPA 392 3 LFGNTTDNGGQYLEGNP AF080248 391 2 MICOLLPTASE4 Length of motif = 19 Motif number = 4 Microbial collagenase motif IV - 1 PCODE ST INT RHEFTHYLQGRYVVPGMWG COLA_CLOPE 501 20 EHEYVHYLDGRFDLYGGFS COLA_VIBAL 476 26 EHEYTHYLDARFNQYGSFS COLA_VIBPA 434 25 EHEYTHYLDARFNQYGSFS AF080248 433 25 MICOLLPTASE5 Length of motif = 16 Motif number = 5 Microbial collagenase motif V - 1 PCODE ST INT GVLTWYEEGTAEFFAG COLA_CLOPE 527 7 EKIVWWSEGIAEYVAQ COLA_VIBAL 498 3 GHIVWWLEGFAEYMHY COLA_VIBPA 458 5 GHIVWWLEGFAEYMHY AF080248 457 5 FINAL MOTIF SETS MICOLLPTASE1 Length of motif = 19 Motif number = 1 Microbial collagenase motif I - 2 PCODE ST INT GIPTLVEFLRAGYYLGFYN COLA_CLOPE 159 159 GMPQLVLYLRAGYYVHYYN O54108 189 189 ELETLFLYLRAGYYAEFYN COLA_VIBAL 144 144 GIPTLVEVVRAGFYLGFHN Q46085 114 114 VLENLGEFVRAAYYVRYNA COLA_VIBPA 97 97 MICOLLPTASE2 Length of motif = 15 Motif number = 2 Microbial collagenase motif II - 2 PCODE ST INT LTVVIYNSPEEYKLN COLA_CLOPE 447 269 IEVVVFDSSTDYQTY O54108 463 255 LQVNIFDSSTDYGKY COLA_VIBAL 415 252 LTMVIYNSPEEYKLN Q46085 400 267 VEVAVFASNDSYVDY COLA_VIBPA 374 258 MICOLLPTASE3 Length of motif = 17 Motif number = 3 Microbial collagenase motif III - 2 PCODE ST INT INGFSTDNGGIYIENIG COLA_CLOPE 464 2 MYGIDTNNGGMYLEGNP O54108 481 3 IFDISTDNGGMYLEGDP COLA_VIBAL 433 3 LYGYDTNNGGMYIEPEG Q46085 417 2 LFGNTTDNGGQYLEGTP COLA_VIBPA 392 3 MICOLLPTASE4 Length of motif = 19 Motif number = 4 Microbial collagenase motif IV - 2 PCODE ST INT RHEFTHYLQGRYVVPGMWG COLA_CLOPE 501 20 NHEYTHYLDGRFDMYGDFN O54108 524 26 EHEYVHYLDGRFDLYGGFS COLA_VIBAL 476 26 RHEYTHYLQGRYAVPGQWG Q46085 454 20 EHEYTHYLDARFNQYGSFS COLA_VIBPA 434 25 MICOLLPTASE5 Length of motif = 16 Motif number = 5 Microbial collagenase motif V - 2 PCODE ST INT GVLTWYEEGTAEFFAG COLA_CLOPE 527 7 TPTIWWVEGFAEYVSY O54108 547 4 EKIVWWSEGIAEYVAQ COLA_VIBAL 498 3 DRLTWYEEGGAELFAG Q46085 480 7 GHIVWWLEGFAEYMHY COLA_VIBPA 458 5
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