1JJ9

Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The 1.8-A crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition.

Brandstetter, H.Grams, F.Glitz, D.Lang, A.Huber, R.Bode, W.Krell, H.W.Engh, R.A.

(2001) J.Biol.Chem. 276: 17405-17412

  • DOI: 10.1074/jbc.M007475200

  • PubMed Abstract: 
  • The individual zinc endoproteinases of the tissue degrading matrix metalloproteinase (MMP) family share a common catalytic architecture but are differentiated with respect to substrate specificity, localization, and activation. Variation in domain st ...

    The individual zinc endoproteinases of the tissue degrading matrix metalloproteinase (MMP) family share a common catalytic architecture but are differentiated with respect to substrate specificity, localization, and activation. Variation in domain structure and more subtle structural differences control their characteristic specificity profiles for substrates from among four distinct classes (Nagase, H., and Woessner, J. F. J. (1999) J. Biol. Chem. 274, 21491-21494). Exploitation of these differences may be decisive for the design of anticancer or other drugs, which should be highly selective for their particular MMP targets. Based on the 1.8-A crystal structure of human neutrophil collagenase (MMP-8) in complex with an active site-directed inhibitor (RO200-1770), we identify and describe new structural determinants for substrate and inhibitor recognition in addition to the primary substrate recognition sites. RO200-1770 induces a major rearrangement at a position relevant to substrate recognition near the MMP-8 active site (Ala206-Asn218). In stromelysin (MMP-3), competing stabilizing interactions at the analogous segment hinder a similar rearrangement, consistent with kinetic profiling of several MMPs. Despite the apparent dissimilarity of the inhibitors, the central 2-hydroxypyrimidine-4,6-dione (barbiturate) ring of the inhibitor RO200-1770 mimics the interactions of the hydroxamate-derived inhibitor batimastat (Grams, F., Reinemer, P., Powers, J. C., Kleine, T., Pieper, M., Tschesche, H., Huber, R., and Bode, W. (1995) Eur. J. Biochem. 228, 830-841) for binding to MMP-8. The two additional phenyl and piperidyl ring substituents of the inhibitor bind into the S1' and S2' pockets of MMP-8, respectively. The crystal lattice contains a hydrogen bond between the O(gamma) group of Ser209 and N(delta)1 of His207 of a symmetry related molecule; this interaction suggests a model for recognition of hydroxyprolines present in physiological substrates. We also identify a collagenase-characteristic cis-peptide bond, Asn188-Tyr189, on a loop essential for collagenolytic activity. The sequence conservation pattern at this position marks this cis-peptide bond as a determinant for triple-helical collagen recognition and processing.


    Organizational Affiliation

    Department of Structural Research, Max Planck Institute for Biochemistry, D-82152 Martinsried, Germany. hbs@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Matrix Metalloproteinase 8
A
163Homo sapiensGene Names: MMP8 (CLG1)
EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens)
Go to Gene View: MMP8
Go to UniProtKB:  P22894
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BBT
Query on BBT

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Download CCD File 
A
2-HYDROXY-5-[4-(2-HYDROXY-ETHYL)-PIPERIDIN-1-YL]-5-PHENYL-1H-PYRIMIDINE-4,6-DIONE
C17 H21 N3 O4
IPBPOBHSNJFRFT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BBTIC50: 1700 nM (100) BINDINGDB
BBTIC50: 1700 nM BINDINGMOAD
BBTIC50: 1700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.020α = 90.00
b = 69.230β = 90.00
c = 88.470γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
X-GENdata reduction
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description