1JAO

COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design.

Grams, F.Reinemer, P.Powers, J.C.Kleine, T.Pieper, M.Tschesche, H.Huber, R.Bode, W.

(1995) Eur.J.Biochem. 228: 830-841

  • Primary Citation of Related Structures:  
  • Also Cited By: 1ZVX, 1ZS0

  • PubMed Abstract: 
  • Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases involved in tissue remodeling. They have also been implicated in various disease processes including tumour invasion and joint destruction and are therefore attractive targets for i ...

    Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases involved in tissue remodeling. They have also been implicated in various disease processes including tumour invasion and joint destruction and are therefore attractive targets for inhibitor design. For rational drug design, information of inhibitor binding at the atomic level is essential. Recently, we have published the refined high-resolution crystal structure of the catalytic domain of human neutrophil collagenase (HNC) complexed with the inhibitor Pro-Leu-Gly-NHOH, which is a mimic for the unprimed (P3-P1) residues of a bound peptide substrate. We have now determined two additional HNC complexes formed with the thiol inhibitor HSCH2CH(CH2Ph)CO-L-Ala-Gly-NH2 and another hydroxamate inhibitor, HONHCOCH(iBu)CO-L-Ala-Gly-NH2, which were both refined to R-values of 0.183/0.198 at 0.240/0.225-nm resolution. The inhibitor thiol and hydroxamate groups ligand the catalytic zinc, giving rise to a slightly distorted tetrahedral and trigonal-bipyramidal coordination sphere, respectively. The thiol inhibitor diastereomer with S-configuration at the P1' residue (corresponding to an L-amino acid analog) binds to HNC. Its peptidyl moiety mimics binding of primed (P1'-P3') residues of the substrate. In combination with our first structure a continuous hexapeptide corresponding to a peptide substrate productively bound to HNC was constructed and energy-minimized. Proteolytic cleavage of this Michaelis complex is probably general base-catalyzed as proposed for thermolysin, i.e. a glutamate assists nucleophilic attack of a water molecule. Although there are many structural and mechanistic similarities to thermolysin, substrate binding to MMPs differs due to the interactions beyond S1'-P1'. While thermolysin binds substrates with a kink at P1', substrates are bound in an extended conformation in the collagenases. This property explains the tolerance of thermolysin for D-amino acid residues at the P1' position, in contrast to the collagenases. The third inhibitor, HONHCOCH(iBu)CO-L-Ala-Gly-NH2, unexpectedly binds in a different manner than anticipated from its design and binding mode in thermolysin. Its hydroxamate group obviously interacts with the catalytic zinc in a favourable bidentate manner, but in contrast its isobutyl (iBu) side chain remains outside of the S1' pocket, presumably due to severe constraints imposed by the adjacent planar hydroxamate group. Instead, the C-terminal Ala-Gly-NH2 tail adopts a bent conformation and inserts into this S1' pocket, presumably in a non-optimized manner. Both the isobutyl side chain and the C-terminal peptide tail could be replaced by other, better fitting groups.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited by a Substrate Analogue Reveals the Essentials for Catalysis and Specificity
      Bode, W.,Reinemer, P.,Huber, R.,Kleine, T.,Schnierer, S.,Tschesche, H.
      (1994) Embo J. 13: 1263
    • Structural Implications for the Role of the N Terminus in the 'Superactivation' of Collagenases. A Crystallographic Study
      Reinemer, P.,Grams, F.,Huber, R.,Kleine, T.,Schnierer, S.,Piper, M.,Tschesche, H.,Bode, W.
      (1994) FEBS Lett. 338: 227


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MATRIX METALLO PROTEINASE-8 (MET80 FORM)
A
163Homo sapiensMutation(s): 0 
Gene 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

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
0D3
Query on 0D3

Download SDF File 
Download CCD File 
A
N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide
C15 H21 N3 O3 S
AUJQAKJLNYFOHT-CMPLNLGQSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000232 (0D3)
Query on PRD_000232
AN-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamidePeptide-like / Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0D3Ki: 1200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.240α = 90.00
b = 69.200β = 90.00
c = 72.330γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
CCP4data scaling
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other