1RM8

Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the catalytic domain of MMP-16/MT3-MMP: characterization of MT-MMP specific features.

Lang, R.Braun, M.Sounni, N.E.Noel, A.Frankenne, F.Foidart, J.M.Bode, W.Maskos, K.

(2004) J Mol Biol 336: 213-225

  • DOI: https://doi.org/10.1016/j.jmb.2003.12.022
  • Primary Citation of Related Structures:  
    1RM8

  • PubMed Abstract: 

    Membrane-type matrix metalloproteinases (MT-MMPs) have attracted strong attention, because four of them can activate a key player in the tumor scenario, proMMP-2/progelatinase A. In addition to this indirect effect on the cellular environment, these MT-MMPs degrade extracellular matrix proteins, and their overproduction is associated with tumor growth. We have solved the structure of the catalytic domain (cd) of MT3-MMP/MMP-16 in complex with the hydroxamic acid inhibitor batimastat. CdMT3-MMP exhibits a classical MMP-fold with similarity to MT1-MMP. Nevertheless, it also shows unique properties such as a modified MT-specific loop and a closed S1' specificity pocket, which might help to design specific inhibitors. Some MT-MMP-specific features, derived from the crystal structures of MT-1-MMP determined previously and MT3-MMP, and revealed in recent mutagenesis experiments, explain the impaired interaction of the MT-MMPs with TIMP-1. Docking experiments with proMMP-2 show some exposed loops including the MT-loop of cdMT3-MMP involved in the interaction with the proMMP-2 prodomain in the activation encounter complex. This model might help to understand the experimentally proven importance of the MT-loop for the activation of proMMP-2.


  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried-bei-munchen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix metalloproteinase-16169Homo sapiensMutation(s): 0 
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P51512 (Homo sapiens)
Explore P51512 
Go to UniProtKB:  P51512
PHAROS:  P51512
GTEx:  ENSG00000156103 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51512
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BAT PDBBind:  1RM8 Ki: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.21α = 90
b = 51.21β = 90
c = 149.368γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-08
    Changes: Structure summary
  • Version 1.4: 2021-07-28
    Changes: Advisory, Derived calculations, Refinement description
  • Version 1.5: 2023-08-23
    Changes: Advisory, Data collection, Database references, Refinement description