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 [1]. Of these, around
half contain the HEXXH motif, which has been shown in crystallographic
studies to form part of the metal-binding site [1]. 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 [1].
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 [1]. 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 [1]. 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[1]. 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
[4]. Clostrium histolyticum is a pathogen that causes gas gangrene;
nevertheless, the isolated collagenase has been used to treat bed sores [5].
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 [6]. 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 [6].
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 3.4.24.3) (120 KD COLLAG
O54108 PUTATIVE SECRETED PROTEASE - STREPTOMYCES COELICOLOR.
COLA_VIBAL MICROBIAL COLLAGENASE PRECURSOR (EC 3.4.24.3) - VIBRIO ALGIN
Q46085 COLLAGENASE PRECURSOR - CLOSTRIDIUM HISTOLYTICUM.
COLA_VIBPA MICROBIAL COLLAGENASE PRECURSOR (EC 3.4.24.3) - 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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