spacer
spacer

PDBsum entry 1ee3

Go to PDB code: 
protein metals links
Hydrolase PDB id
1ee3
Jmol
Contents
Protein chain
305 a.a. *
Metals
_CD ×4
Waters ×245
* Residue conservation analysis
PDB id:
1ee3
Name: Hydrolase
Title: Cadmium-substituted bovine pancreatic carboxypeptidase a (alfa-form) at ph 7.5 and 2 mm chloride in monoclinic crystal form
Structure: Protein (carboxypeptidase a). Chain: p. Ec: 3.4.17.1
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.70Å     R-factor:   0.174     R-free:   0.198
Authors: F.Jensen,T.Bukrinsky,J.Bjerrum,S.Larsen
Key ref: F.Jensen et al. (2002). Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function. J Biol Inorg Chem, 7, 490-499. PubMed id: 11941507 DOI: 10.1007/s00775-001-0324-0
Date:
30-Jan-00     Release date:   26-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00730  (CBPA1_BOVIN) -  Carboxypeptidase A1
Seq:
Struc:
419 a.a.
305 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.1  - Carboxypeptidase A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidyl-L-amino acid + H2O = peptide + L-amino acid

+
=
+
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     zinc ion binding     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1007/s00775-001-0324-0 J Biol Inorg Chem 7:490-499 (2002)
PubMed id: 11941507  
 
 
Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function.
F.Jensen, T.Bukrinsky, J.Bjerrum, S.Larsen.
 
  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) 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19244162 M.J.Heeb, D.Prashun, J.H.Griffin, and B.N.Bouma (2009).
Plasma protein S contains zinc essential for efficient activated protein C-independent anticoagulant activity and binding to factor Xa, but not for efficient binding to tissue factor pathway inhibitor.
  FASEB J, 23, 2244-2253.  
17391648 J.R.Hershfield, N.Pattabiraman, C.N.Madhavarao, and M.A.Namboodiri (2007).
Mutational analysis of aspartoacylase: implications for Canavan disease.
  Brain Res, 1148, 1.  
12598656 A.J.Stewart, C.A.Blindauer, S.Berezenko, D.Sleep, and P.J.Sadler (2003).
Interdomain zinc site on human albumin.
  Proc Natl Acad Sci U S A, 100, 3701-3706.  
12777760 K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.Poulsen, P.Schneider, J.Vind, and S.Larsen (2003).
Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.
  Acta Crystallogr D Biol Crystallogr, 59, 989-996.
PDB codes: 1h3j 1ly9 1lyc 1lyk
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.