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PDBsum entry 2oy2

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protein ligands metals links
Hydrolase PDB id
2oy2
Jmol
Contents
Protein chain
157 a.a. *
Ligands
ILE-ALA-GLY ×2
Metals
_ZN ×4
_CA ×4
Waters ×565
* Residue conservation analysis
PDB id:
2oy2
Name: Hydrolase
Title: Human mmp-8 in complex with peptide iag
Structure: Neutrophil collagenase. Chain: a, f. Fragment: catalytic domain. Synonym: matrix metalloproteinase-8, mmp-8, pmnl collagenase, pmnl-cl. Engineered: yes. Ile-ala-gly peptide. Chain: w, y. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: mmp8, clg1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
Resolution:
1.50Å     R-factor:   0.166     R-free:   0.192
Authors: V.Calderone,I.Bertini,M.Fragai,C.Luchinat,M.Maletta,K.J.Yeo
Key ref: I.Bertini et al. (2006). Snapshots of the reaction mechanism of matrix metalloproteinases. Angew Chem Int Ed Engl, 45, 7952-7955. PubMed id: 17096442
Date:
21-Feb-07     Release date:   06-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22894  (MMP8_HUMAN) -  Neutrophil collagenase
Seq:
Struc:
467 a.a.
157 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.34  - Neutrophil collagenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage of interstitial collagens in the triple helical domain. Unlike EC 3.4.24.7, this enzyme cleaves type III collagen more slowly than type I.
      Cofactor: Ca(2+); Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular matrix   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     metallopeptidase activity     3 terms  

 

 
Angew Chem Int Ed Engl 45:7952-7955 (2006)
PubMed id: 17096442  
 
 
Snapshots of the reaction mechanism of matrix metalloproteinases.
I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19609998 I.Bertini, M.Fragai, C.Luchinat, M.Melikian, and C.Venturi (2009).
Characterisation of the MMP-12-elastin adduct.
  Chemistry, 15, 7842-7845.  
19282283 I.Bertini, M.Fragai, C.Luchinat, M.Melikian, E.Mylonas, N.Sarti, and D.I.Svergun (2009).
Interdomain Flexibility in Full-length Matrix Metalloproteinase-1 (MMP-1).
  J Biol Chem, 284, 12821-12828.  
19707688 M.Rouffet, C.Denhez, E.Bourguet, F.Bohr, and D.Guillaume (2009).
In silico study of MMP inhibition.
  Org Biomol Chem, 7, 3817-3825.  
19131516 P.J.Baker, K.L.Britton, M.Fisher, J.Esclapez, C.Pire, M.J.Bonete, J.Ferrer, and D.W.Rice (2009).
Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily.
  Proc Natl Acad Sci U S A, 106, 779-784.
PDB codes: 2vwg 2vwh 2vwp 2vwq
18604568 C.Andreini, I.Bertini, G.Cavallaro, G.L.Holliday, and J.M.Thornton (2008).
Metal ions in biological catalysis: from enzyme databases to general principles.
  J Biol Inorg Chem, 13, 1205-1218.  
17963710 I.Sagi, and M.E.Milla (2008).
Application of structural dynamic approaches provide novel insights into the enzymatic mechanism of the tumor necrosis factor-alpha-converting enzyme.
  Anal Biochem, 372, 1.  
18539597 R.Bhaskaran, M.O.Palmier, J.L.Lauer-Fields, G.B.Fields, and S.R.Van Doren (2008).
MMP-12 catalytic domain recognizes triple helical peptide models of collagen V with exosites and high activity.
  J Biol Chem, 283, 21779-21788.  
17710450 L.A.Alcaraz, L.Banci, I.Bertini, F.Cantini, A.Donaire, and L.Gonnelli (2007).
Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors.
  J Biol Inorg Chem, 12, 1197-1206.
PDB codes: 2jnp 2jt5 2jt6
17997411 R.Bhaskaran, M.O.Palmier, N.A.Bagegni, X.Liang, and S.R.Van Doren (2007).
Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment.
  J Mol Biol, 374, 1333-1344.
PDB code: 2poj
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.