PDBsum entry 1cxv

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
160 a.a. *
CBP ×2
_ZN ×4
_CA ×4
Waters ×321
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of recombinant mouse collagenase-3 (mmp-13)
Structure: Protein (collagenase-3). Chain: a, b. Fragment: catalytic domain. Synonym: matrix metalloproteinase, mmp-13. Ec: 3.4.24.-
Source: Mus musculus. House mouse. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.196     R-free:   0.234
Authors: I.Botos,E.Meyer,S.M.Swanson,V.Lemaitre,Y.Eeckhout,E.F.Meyer
Key ref:
I.Botos et al. (1999). Structure of recombinant mouse collagenase-3 (MMP-13). J Mol Biol, 292, 837-844. PubMed id: 10525409 DOI: 10.1006/jmbi.1999.3068
30-Aug-99     Release date:   30-Aug-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P33435  (MMP13_MOUSE) -  Collagenase 3
472 a.a.
160 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     collagen catabolic process   2 terms 
  Biochemical function     metallopeptidase activity     3 terms  


DOI no: 10.1006/jmbi.1999.3068 J Mol Biol 292:837-844 (1999)
PubMed id: 10525409  
Structure of recombinant mouse collagenase-3 (MMP-13).
I.Botos, E.Meyer, S.M.Swanson, V.Lemaître, Y.Eeckhout, E.F.Meyer.
The matrix metalloproteinases are crucial in the physiological and pathological degradation of the mammalian extracellular matrix, including breast tumours, and osteoarthritic cartilage. These enzymes are classified according to their matrix substrate specificity. Collagenase-3 (MMP-13) is a member of this family and preferentially cleaves type II collagen, cartilage, fibronectin and aggrecan. Collagenase-3 is normally expressed in hypertrophic chondrocytes, periosteal cells, and osteoblasts during bone development. The structure of the catalytic domain of recombinant mouse collagenase-3, complexed to the hydroxamate inhibitor (RS-113456), is reported at 2.0 A resolution. Molecular replacement and weak phasing information from a single derivative determined the structure. Neither molecular replacement nor derivative methods had a sufficient radius of convergence to yield a refinable structure. The structure illuminates the atomic zinc ion interactions with functional groups in the active site, emphasizing zinc ligation and the very voluminous hydrophobic P1' group for the inhibitor potency. The structure provides insight into the specificity of this enzyme, facilitating design of specific inhibitors to target various diseases.
  Selected figure(s)  
Figure 1.
Figure 1. Ribbon diagram of collagenase-3 with the catalytic and structural zinc atoms (blue spheres), the structural calcium atoms (red spheres) and the bound RS-113456 inhibitor. Figure created with SPOCK [Christopher 1998] and rendered with Raster-3D [Bacon and Anderson 1988 and Merritt and Murphy 1994].
Figure 3.
Figure 3. Stereo view of active site region with the catalytic zinc atom (blue sphere), ligating histidine residues and bound inhibitor. Omit map contoured at 2.0 s. Figure created with SPOCK.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 292, 837-844) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15965736 C.H.Penhoat, Z.Li, H.S.Atreya, S.Kim, A.Yee, R.Xiao, D.Murray, C.H.Arrowsmith, and T.Szyperski (2005).
NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.
  J Struct Funct Genomics, 6, 51-62.
PDB code: 1tvi
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 code is shown on the right.