2E2D

Flexibility and variability of TIMP binding: X-ray structure of the complex between collagenase-3/MMP-13 and TIMP-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Flexibility and Variability of TIMP Binding: X-ray Structure of the Complex Between Collagenase-3/MMP-13 and TIMP-2

Maskos, K.Lang, R.Tschesche, H.Bode, W.

(2007) J.Mol.Biol. 366: 1222-1231

  • DOI: 10.1016/j.jmb.2006.11.072

  • PubMed Abstract: 
  • The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of f ...

    The excessive activity of matrix metalloproteinases (MMPs) contributes to pathological processes such as arthritis, tumor growth and metastasis if not balanced by the tissue inhibitors of metalloproteinases (TIMPs). In arthritis, the destruction of fibrillar (type II) collagen is one of the hallmarks, with MMP-1 (collagenase-1) and MMP-13 (collagenase-3) being identified as key players in arthritic cartilage. MMP-13, furthermore, has been found in highly metastatic tumors. We have solved the 2.0 A crystal structure of the complex between the catalytic domain of human MMP-13 (cdMMP-13) and bovine TIMP-2. The overall structure resembles our previously determined MT1-MMP/TIMP-2 complex, in that the wedge-shaped TIMP-2 inserts with its edge into the entire MMP-13 active site cleft. However, the inhibitor is, according to a relative rotation of approximately 20 degrees, oriented differently relative to the proteinase. Upon TIMP binding, the catalytic zinc, the zinc-ligating side chains, the enclosing MMP loop and the S1' wall-forming segment move significantly and in concert relative to the rest of the cognate MMP, and the active site cleft constricts slightly, probably allowing a more favourable interaction between the Cys1(TIMP) alpha-amino group of the inhibitor and the catalytic zinc ion of the enzyme. Thus, this structure supports the view that the central N-terminal TIMP segment essentially defines the relative positioning of the TIMP, while the flanking edge loops determine the relative orientation, depending on the individual target MMP.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Forschungsgruppe Proteinasen, Am Klopferspitz 18, D-82152 Martinsried, Germany. maskos@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matrix metallopeptidase 13
A
165Homo sapiensMutation(s): 0 
Gene Names: MMP13
EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens)
Go to Gene View: MMP13
Go to UniProtKB:  P45452
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metalloproteinase inhibitor 2
C
180Bos taurusMutation(s): 0 
Gene Names: TIMP2
Find proteins for P16368 (Bos taurus)
Go to Gene View: TIMP2
Go to UniProtKB:  P16368
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 72.526α = 90.00
b = 72.526β = 90.00
c = 181.375γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
DNAdata collection
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance