1EE3

Cadmium-substituted bovine pancreatic carboxypeptidase A (alfa-form) at pH 7.5 and 2 mM chloride in monoclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function

Jensen, F.Bukrinsky, T.Bjerrum, J.Larsen, S.

(2002) J.BIOL.INORG.CHEM. 7: 490-499

  • DOI: 10.1007/s00775-001-0324-0
  • Primary Citation of Related Structures:  1ELL, 1ELM

  • PubMed Abstract: 
  • Three high-resolution crystal structures of Cd(II)-substituted carboxypeptidase A (CPA) have been determined by X-ray diffraction from crystals prepared in three different buffer systems to assess the effect of pH and ionic strength on the Cd(II) coo ...

    Three high-resolution crystal structures of Cd(II)-substituted carboxypeptidase A (CPA) have been determined by X-ray diffraction from crystals prepared in three different buffer systems to assess the effect of pH and ionic strength on the Cd(II) coordination geometry. All crystallize in the space group P2(1) with identical cell dimensions. Cd-CPA(7.5): Cd(II)-substituted CPA prepared at pH 7.5 with [Cl(-)]=2 mM determined to 1.70 A resolution ( R=17.4% and R(free)=19.8%); Cd-CPA(5.5): Cd(II)-substituted CPA prepared at pH 5.5 with [Cl(-)]=2 mM to 2.00 A resolution ( R=16.1% and R(free)=18.6%); Cd-CPA(7.5)-Cl: Cd(II)-substituted CPA prepared at pH 7.5 with [Cl(-)]=250 mM to 1.76 A resolution ( R=16.7% and R(free)=17.8%). No noticeable structural changes were observed between the three structures. Two water molecules coordinate to Cd(II), in contrast to the single water molecule coordinating to Zn(II) in the Zn-CPA structure. No binding sites for anions could be identified, even in the structure with a high concentration of chloride ions. It is suggested that the anion inhibition is due to weak outer-sphere association of Cl(-) ions at several binding sites, shielding the strong positive charge distribution at the surface of the protein near the active site. Based on structural data and a sequence alignment of 18 non-redundant carboxypeptidases, a more elaborate version of the earlier reaction model is proposed that also addresses the transport of water to and from the active site. Conserved residues whose function was not addressed previously delineate the proposed pathways used in the transport of water during catalysis.


    Related Citations: 
    • Native Carboxypeptidase A in a New Crystal Environment Reveals A Different Conformation of the Important Tyrosine 248
      Bukrinsky, J.T.,Bjerrum, M.T.,Kadziola, A.
      (1998) Biochemistry 37: 16555
    • Carboxypeptidase A: Native, Zinc-Removed and Mercury-Replaced Forms
      Greenblatt, H.M.,Feinberg, H.,Tucker, P.A.,Shoham, G.
      (1998) Acta Crystallogr.,Sect.D 54: 289
    • Structure and Dynamics of the Metal Site of Cadmium-substituted Carboxypeptidase A in Solution and Crystalline States and under Steady-State Peptide Hydrolysis
      Bauer, R.,Danielsen, E.,Hemmingsen, L.,Soerensen, M.V.,Ulstrup, J.,Friis, E.P.,Auld, D.S.,Bjerrum, M.J.
      (1997) Biochemistry 36: 11514


    Organizational Affiliation

    Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CARBOXYPEPTIDASE A)
P
309Bos taurusGene 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
P
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.178α = 90.00
b = 60.205β = 97.46
c = 51.715γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-26
    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: Refinement description