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Collagenase Provide feedback
This family of enzymes break down collagens.
Matsushita O, Yoshihara K, Katayama S, Minami J, Okabe A; , J Bacteriol 1994;176:149-156.: Purification and characterization of Clostridium perfringens 120- kilodalton collagenase and nucleotide sequence of the corresponding gene. PUBMED:8282691 EPMC:8282691
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This tab holds annotation information from the InterPro database.
InterPro entry IPR002169
Over 50 metallopeptidase families have been identified to date. In these enzymes, a divalent cation, usually zinc but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site [PUBMED:7674922]. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases 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 [PUBMED:7674922].
This entry represents sequences belonging to peptidase family M9, subfamilies M9A and M9B (microbial collagenase, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH [PUBMED:7674922].
Microbial collagenases have been identified from bacteria of both the Vibrio and Clostridium genuses. 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. Clostridium 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.
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 [PUBMED:8282691]. 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 [PUBMED:8282691].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Molecular function||serine-type endopeptidase activity (GO:0004252)|
|zinc ion binding (GO:0008270)|
|Biological process||proteolysis (GO:0006508)|
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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Clan MA is one of two zinc-dependent metallopeptidases that contain the HEXXH motif. The two histidines are zinc ligands. The structures of this clan show the active site is between its two sub-domains.
The clan contains the following 71 members:Aminopep Aspzincin_M35 Astacin ATLF BSP DA1-like DUF1570 DUF2201_N DUF2268 DUF3152 DUF3267 DUF3810 DUF3920 DUF4157 DUF4344 DUF45 DUF4953 DUF885 HRXXH Metallopep Peptidase_M1 Peptidase_M10 Peptidase_M11 Peptidase_M13 Peptidase_M2 Peptidase_M27 Peptidase_M3 Peptidase_M30 Peptidase_M32 Peptidase_M35 Peptidase_M36 Peptidase_M4 Peptidase_M41 Peptidase_M43 Peptidase_M48 Peptidase_M49 Peptidase_M4_C Peptidase_M50 Peptidase_M50B Peptidase_M54 Peptidase_M56 Peptidase_M57 Peptidase_M6 Peptidase_M60 Peptidase_M61 Peptidase_M64 Peptidase_M66 Peptidase_M7 Peptidase_M76 Peptidase_M78 Peptidase_M8 Peptidase_M85 Peptidase_M9 Peptidase_M90 Peptidase_M91 Peptidase_MA_2 Peptidase_Mx Peptidase_Mx1 Peptidase_U49 Reprolysin Reprolysin_2 Reprolysin_3 Reprolysin_4 Reprolysin_5 SprT-like UPF0054 WLM Zincin_1 Zincin_2 Zn_peptidase Zn_peptidase_2
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||27|
|Number in full:||255|
|Average length of the domain:||285.40 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||36.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_M9 domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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