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PDBsum entry 3dsl

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3dsl
Jmol
Contents
Protein chains
416 a.a. *
Ligands
NAG
FLE-TRP ×2
Metals
_ZN ×2
_CA ×6
Waters ×184
* Residue conservation analysis
PDB id:
3dsl
Name: Hydrolase
Title: The three-dimensional structure of bothropasin, the main hem factor from bothrops jararaca venom.
Structure: Zinc metalloproteinase-disintegrin bothropasin. Chain: a, b. Synonym: disintegrin bothropasin. Ec: 3.4.24.49
Source: Bothrops jararaca. Jararaca. Organism_taxid: 8724
Resolution:
2.70Å     R-factor:   0.217     R-free:   0.294
Authors: J.R.C.Muniz,A.Ambrosio,H.S.Selistre-De-Araujo,G.Oliva,R.C.Ga D.H.F.Souza
Key ref: J.R.Muniz et al. (2008). The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: insights for a new classification of snake venom metalloprotease subgroups. Toxicon, 52, 807-816. PubMed id: 18831982 DOI: 10.1016/j.toxicon.2008.08.021
Date:
13-Jul-08     Release date:   21-Oct-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O93523  (VM3BP_BOTJA) -  Zinc metalloproteinase-disintegrin-like bothropasin
Seq:
Struc:
 
Seq:
Struc:
610 a.a.
416 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.49  - Bothropasin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage of 5-His-|-Leu-6, 10-His-|-Leu-11, 14-Ala-|-Leu-15, 16-Tyr-|-Leu-17 and 24-Phe-|-Phe-25 in insulin B chain.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metallopeptidase activity     2 terms  

 

 
DOI no: 10.1016/j.toxicon.2008.08.021 Toxicon 52:807-816 (2008)
PubMed id: 18831982  
 
 
The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: insights for a new classification of snake venom metalloprotease subgroups.
J.R.Muniz, A.L.Ambrosio, H.S.Selistre-de-Araujo, M.R.Cominetti, A.M.Moura-da-Silva, G.Oliva, R.C.Garratt, D.H.Souza.
 
  ABSTRACT  
 
Bothropasin is a 48kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys189 is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from PII SVMPs. The ECD motif is stabilized by the Cys277-Cys310 disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu276 of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other PIII SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other PIII members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain.