1C3I

HUMAN STROMELYSIN-1 CATALYTIC DOMAIN COMPLEXED WITH RO-26-2812

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Expression, characterization and structure determination of an active site mutant (Glu202-Gln) of mini-stromelysin-1.

Steele, D.L., El-Kabbani, O., Dunten, P., Windsor, L.J., Kammlott, R.U., Crowther, R.L., Michoud, C., Engler, J.A., Birktoft, J.J.

(2000) Protein Eng. 13: 397-405

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human stromelysin-1 is a member of the matrix metalloproteinase (MMP) family of enzymes. The active site glutamic acid of the MMPs is conserved throughout the family and plays a pivotal role in the catalytic mechanism. The structural and functional c ...

    Human stromelysin-1 is a member of the matrix metalloproteinase (MMP) family of enzymes. The active site glutamic acid of the MMPs is conserved throughout the family and plays a pivotal role in the catalytic mechanism. The structural and functional consequences of a glutamate to glutamine substitution in the active site of stromelysin-1 were investigated in this study. In contrast to the wild-type enzyme, the glutamine-substituted mutant was not active in a zymogram assay where gelatin was the substrate, was not activated by organomercurials and showed no activity against a peptide substrate. The glutamine-substituted mutant did, however, bind to TIMP-1, the tissue inhibitor of metalloproteinases, after cleavage of the propeptide with trypsin. A second construct containing the glutamine substitution but lacking the propeptide was also inactive in the proteolysis assays and capable of TIMP-1 binding. X-ray structures of the wild-type and mutant proteins complexed with the propeptide-based inhibitor Ro-26-2812 were solved and in both structures the inhibitor binds in an orientation the reverse of that of the propeptide in the pro-form of the enzyme. The inhibitor makes no specific interactions with the active site glutamate and a comparison of the wild-type and mutant structures revealed no major structural changes resulting from the glutamate to glutamine substitution.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Genetics, Oral Cancer Research Center and Research Center in Oral Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1
A, B
173Homo sapiensMutation(s): 0 
Gene Names: MMP3 (STMY1)
EC: 3.4.24.17
Find proteins for P08254 (Homo sapiens)
Go to Gene View: MMP3
Go to UniProtKB:  P08254
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TR1
Query on TR1
Download SDF File 
Download CCD File 
B
2-(2-{2-[(BIPHENYL-4-YLMETHYL)-AMINO]-3-MERCAPTO-PENTANOYLAMINO}-ACETYLAMINO)-3-METHYL-BUTYRIC ACID METHYL ESTER
C24 H31 N3 O4 S
QFAWBPLETHINFK-UNMCSNQZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TR1IC50: 1600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.730α = 90.00
b = 78.060β = 90.00
c = 105.740γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
SDMSdata scaling
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance