6CPA

CRYSTAL STRUCTURE OF THE COMPLEX OF CARBOXYPEPTIDASE A WITH A STRONGLY BOUND PHOSPHONATE IN A NEW CRYSTALLINE FORM: COMPARISON WITH STRUCTURES OF OTHER COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.

Kim, H.Lipscomb, W.N.

(1990) Biochemistry 29: 5546-5555

  • DOI: 10.1021/bi00475a019
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity ...

    O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.


    Related Citations: 
    • Phosphonate Analogues of Carboxypeptidasea Substrates are Potent Transition-State Analogue Inhibitors
      Hanson, J.E., Kaplan, A.P., Bartlett, P.A.
      (1989) Biochemistry 28: 6294
    • Refined Crystal Structure of Carboxypeptidasea at 1.54 Angstroms Resolution
      Rees, D.C., Lewis, M., Lipscomb, W.N.
      (1983) J Mol Biol 168: 367

    Organizational Affiliation

    Gibbs Chemical Laboratory, Harvard University, Cambridge, Massachusetts 02138.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE A
A
307Bos taurusMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to UniProtKB:  P00730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZAF
Query on ZAF

Download CCD File 
A
O-(((1R)-((N-PHENYLMETHOXYCARBONYL-L-ALANYL)AMINO)ETHYL)HYDROXYPHOSPHONO)-L-BENZYLACETIC ACID
C22 H27 N2 O8 P
UPJNMOBJDSFRTI-FCEWJHQRSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZAFKi :  0.003000000026077032   nM  PDBBind
ZAFKi:  0.003000000026077032   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.9α = 90
b = 67.2β = 90
c = 76.2γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance