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PDBsum entry 1yme

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protein metals links
Carboxypeptidase PDB id
1yme
Jmol
Contents
Protein chain
307 a.a. *
Metals
_ZN
Waters ×213
* Residue conservation analysis
PDB id:
1yme
Name: Carboxypeptidase
Title: Structure of carboxypeptidase
Structure: Carboxypeptidase a alpha. Chain: a. Synonym: cpa, cox. Other_details: metalloenzyme (zn)
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.53Å     R-factor:   0.148    
Authors: H.M.Greenblatt,P.A.Tucker,G.Shoham
Key ref:
H.M.Greenblatt et al. (1998). Carboxypeptidase A: native, zinc-removed and mercury-replaced forms. Acta Crystallogr D Biol Crystallogr, 54, 289-305. PubMed id: 9867434 DOI: 10.1107/S0907444997010445
Date:
15-Jul-96     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00730  (CBPA1_BOVIN) -  Carboxypeptidase A1
Seq:
Struc:
419 a.a.
307 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: Zinc
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: 10.1107/S0907444997010445 Acta Crystallogr D Biol Crystallogr 54:289-305 (1998)
PubMed id: 9867434  
 
 
Carboxypeptidase A: native, zinc-removed and mercury-replaced forms.
H.M.Greenblatt, H.Feinberg, P.A.Tucker, G.Shoham.
 
  ABSTRACT  
 
The crystal structure of the zinc-containing exopeptidase bovine carboxypeptidase A (CPA) has been refined to high resolution, based on a data set collected from a single crystal, incorporating new sequence information based on cloning of the bovine gene. In addition, new refined structures are available for the zinc-removed form of the enzyme, apo-CPA, as well as the mercury-replaced form, Hg-CPA. The native structure reveals that the zinc-bound water molecule does not appear to more loosely bound than the rest of the zinc ligands, at least when B-factor values are considered. Nor is there any evidence for a secondary location of this water molecule. The apo-enzyme structure does not show any density in the place of the removed zinc ion. The only significant change appears to be a chi2 rotation of one zinc histidine ligand to form an ion-pair interaction with a glutamic acid side chain. The structure of Hg-CPA reveals a solvent Tris molecule bound to the mercury cation, as well as an unidentified cation bound to Glu270. The location of this citation agrees with previous proposals for the binding side of inhibitory zinc. These observations may explain some of the differences in kinetics observed in metal- replaced CPA.
 
  Selected figure(s)  
 
Figure 12.
Figure 12 Active site of Hg-CPA, showing Tris molecule bound to Hg-CPA and another cation (labelled ION) bound to Glu270. The distance between the cation and Glu270 O 2 is 2.5 , and to Glu270 O 1 is 3.5 . The distances of the Tris hydroxyl groups to various side chains in the active site are as follows: to Tyr198 N, 2.5 ; to Arg71 N 2, 2.8 ; to Tyr248 O , 3.5 .
Figure 14.
Figure 14 Plot of R factor versus resolution (PROLSQ refinement) for two data sets from the DIP-100 (apo-CPA and Hg-CPA), and the native CPA data sets from the R-AXIS (monochromator).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1998, 54, 289-305) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16927295 A.Passerini, M.Punta, A.Ceroni, B.Rost, and P.Frasconi (2006).
Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.
  Proteins, 65, 305-316.  
15726624 M.Babor, H.M.Greenblatt, M.Edelman, and V.Sobolev (2005).
Flexibility of metal binding sites in proteins on a database scale.
  Proteins, 59, 221-230.  
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.