3I1U

Carboxypeptidase A Inhibited by a Thiirane Mechanism-Based inactivator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.391 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-ray structure of carboxypeptidase A inhibited by a thiirane mechanism-based inhibitor

Fernandez, D.Testero, S.Vendrell, J.Aviles, F.X.Mobashery, S.

(2010) Chem.Biol.Drug Des. 75: 29-34

  • DOI: 10.1111/j.1747-0285.2009.00907.x

  • PubMed Abstract: 
  • The three-dimensional X-ray crystal structure of carboxypeptidase A, a zinc-dependent hydrolase, covalently modified by a mechanism-based thiirane inactivator, 2-benzyl-3,4-epithiobutanoic acid, has been solved to 1.38 A resolution. The interaction o ...

    The three-dimensional X-ray crystal structure of carboxypeptidase A, a zinc-dependent hydrolase, covalently modified by a mechanism-based thiirane inactivator, 2-benzyl-3,4-epithiobutanoic acid, has been solved to 1.38 A resolution. The interaction of the thiirane moiety of the inhibitor with the active site zinc ion promotes its covalent modification of Glu-270 with the attendant opening of the thiirane ring. The crystal structure determination at high resolution allowed for the clear visualization of the covalent ester bond to the glutamate side chain. The newly generated thiol from the inhibitor binds to the catalytic zinc ion in a monodentate manner, inducing a change in the zinc ion geometry and coordination, while its benzyl group fits into the S1' specificity pocket of the enzyme. The inhibitor molecule is distorted at the position of the carbon atom that is involved in the ester bond linkage on one side and the zinc coordination on the other. This particular type of thiirane-based metalloprotease inhibitor is for the first time analyzed in complex to the target protease at high resolution and may be used as a general model for zinc-dependent proteases.


    Organizational Affiliation

    Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A1 (Pancreatic)
A
309Bos taurusMutation(s): 0 
Gene Names: CPA1 (CPA)
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to Gene View: CPA1
Go to UniProtKB:  P00730
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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BTW
Query on BTW

Download SDF File 
Download CCD File 
A
(2S,3R)-2-benzyl-3-sulfanylbutanoic acid
(2S,3R)-2-benzyl-3-mercaptobutanoic acid
C11 H14 O2 S
LYLMADGMEFUMHJ-PSASIEDQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.391 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.319α = 90.00
b = 57.504β = 99.14
c = 57.080γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-06-28 
  • Released Date: 2009-11-17 
  • Deposition Author(s): Fernandez, D.

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references