1SLN

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-702,842


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Stromelysin-1: three-dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme.

Becker, J.W.Marcy, A.I.Rokosz, L.L.Axel, M.G.Burbaum, J.J.Fitzgerald, P.M.Cameron, P.M.Esser, C.K.Hagmann, W.K.Hermes, J.D.Springer, J.P.

(1995) Protein Sci. 4: 1966-1976

  • DOI: 10.1002/pro.5560041002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proteolytic enzyme stromelysin-1 is a member of the family of matrix metalloproteinases and is believed to play a role in pathological conditions such as arthritis and tumor invasion. Stromelysin-1 is synthesized as a pro-enzyme that is activated ...

    The proteolytic enzyme stromelysin-1 is a member of the family of matrix metalloproteinases and is believed to play a role in pathological conditions such as arthritis and tumor invasion. Stromelysin-1 is synthesized as a pro-enzyme that is activated by removal of an N-terminal prodomain. The active enzyme contains a catalytic domain and a C-terminal hemopexin domain believed to participate in macromolecular substrate recognition. We have determined the three-dimensional structures of both a C-truncated form of the proenzyme and an inhibited complex of the catalytic domain by X-ray diffraction analysis. The catalytic core is very similar in the two forms and is similar to the homologous domain in fibroblast and neutrophil collagenases, as well as to the stromelysin structure determined by NMR. The prodomain is a separate folding unit containing three alpha-helices and an extended peptide that lies in the active site of the enzyme. Surprisingly, the amino-to-carboxyl direction of this peptide chain is opposite to that adopted by the inhibitor and by previously reported inhibitors of collagenase. Comparison of the active site of stromelysin with that of thermolysin reveals that most of the residues proposed to play significant roles in the enzymatic mechanism of thermolysin have equivalents in stromelysin, but that three residues implicated in the catalytic mechanism of thermolysin are not represented in stromelysin.


    Related Citations: 
    • The NMR Structure of the Inhibited Catalytic Domain of Human Stromelysin-1
      Gooley, P.R.,O'Connell, J.F.,Marcy, A.I.,Cuca, G.C.,Salowe, S.P.,Bush, B.L.,Hermes, J.D.,Esser, C.K.,Hagmann, W.K.,Springer, J.P.,Johnson, B.A.
      (1994) Nat.Struct.Mol.Biol. 1: 111
    • Inhibition of Matrix Metalloproteinases by N-Carboxyalkyl Peptides
      Chapman, K.T.,Kopka, I.E.,Durette, P.L.,Esser, C.K.,Lanza, T.J.,Izquierdo-Martin, M.,Niedzwiecki, L.,Chang, B.,Harrison, R.K.,Kuo, D.W.,Lin, T.-T.,Stein, R.L.,Hagmann, W.K.
      (1993) J.Med.Chem. 36: 4293
    • Human Fibroblast Stromelysin Catalytic Domain: Expression, Purification, and Characterization of a C-Terminally Truncated Form
      Marcy, A.I.,Eiberger, L.L.,Harrison, R.,Chan, H.K.,Hutchinson, N.I.,Hagmann, W.K.,Cameron, P.M.,Boulton, D.A.,Hermes, J.D.
      (1991) Biochemistry 30: 6476


    Organizational Affiliation

    Department of Molecular Design and Diversity, Merck Research Laboratories, Rahway, New Jersey 07065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STROMELYSIN-1
A
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
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
INH
Query on INH

Download SDF File 
Download CCD File 
A
N-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)GLYCYL-L-ARGININE-N-PHENYLAMIDE
C25 H35 N6 O4
HDGWGGCPTVXRNA-QMMLZNLJSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INHKi: 230 nM BINDINGMOAD
INHKi: 230 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.230α = 90.00
b = 47.230β = 90.00
c = 150.850γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-08-03 
  • Released Date: 1996-12-17 
  • Deposition Author(s): Becker, J.W.

Revision History 

  • Version 1.0: 1996-12-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2012-02-29
    Type: Database references
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other