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PDBsum entry 1m4l

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protein metals links
Hydrolase PDB id
1m4l
Jmol
Contents
Protein chain
307 a.a. *
Metals
_ZN
Waters ×375
* Residue conservation analysis
PDB id:
1m4l
Name: Hydrolase
Title: Structure of native carboxypeptidase a at 1.25 resolution
Structure: Carboxypeptidase a. Chain: a. Ec: 3.4.17.1
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.25Å     R-factor:   0.104     R-free:   0.145
Authors: A.Kilshtain-Vardi,M.Glick,H.M.Greenblatt,A.Goldblum,G.Shoham
Key ref:
A.Kilshtain-Vardi et al. (2003). Refined structure of bovine carboxypeptidase A at 1.25 A resolution. Acta Crystallogr D Biol Crystallogr, 59, 323-333. PubMed id: 12554943 DOI: 10.1107/S0907444902015706
Date:
03-Jul-02     Release date:   10-Jan-03    
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: 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: 10.1107/S0907444902015706 Acta Crystallogr D Biol Crystallogr 59:323-333 (2003)
PubMed id: 12554943  
 
 
Refined structure of bovine carboxypeptidase A at 1.25 A resolution.
A.Kilshtain-Vardi, M.Glick, H.M.Greenblatt, A.Goldblum, G.Shoham.
 
  ABSTRACT  
 
The crystal structure of the bovine zinc metalloproteinase carboxypeptidase A (CPA) has been refined to 1.25 A resolution based on room-temperature X-ray synchrotron data. The significantly improved structure of CPA at this resolution (anisotropic temperature factors, R factor = 10.4%, R(free) = 14.5%) allowed the modelling of conformational disorders of side chains, improved the description of the protein solvent network (375 water molecules) and provided a more accurate picture of the interactions between the active-site zinc and its ligands. The calculation of standard uncertainties in individual atom positions of the refined model of CPA allowed the deduction of the protonation state of some key residues in the active site and confirmed that Glu72 and Glu270 are negatively charged in the resting state of the enzyme at pH 7.5. These results were further validated by theoretical calculations that showed significant reduction of the pK(a) of these side chains relative to solution values. The distance between the zinc-bound solvent molecule and the metal ion is strongly suggestive of a neutral water molecule and not a hydroxide ion in the resting state of the enzyme. These findings could support both the general acid/general base mechanism, as well as the anhydride mechanism suggested for CPA.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Electron-density `omit' map around the active site of native CPA at 1.25 resolution. Electron-density contour levels are at +4.5 (cyan). Superimposed on the density is the final 1.25 model of CPA (ball-and-stick representation, common atom colour codes), featuring the zinc and its ligands, as well as the catalytic residues Arg127 and Glu270.
Figure 5.
Figure 5 A stereoview of the active site of native CPA (stick model) following the proton-addition algorithm. Atoms are coloured according to conventional codes (C atoms, yellow; N atoms, blue; O atoms, red; H atoms, white; Zn atoms, purple). Zinc-ligand interactions are indicated (dashed lines) and their distances are displayed (). The zinc-bound water is indicated by `W'.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 323-333) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20104355 M.A.Zoroddu, S.Medici, M.Peana, and R.Anedda (2010).
NMR studies of zinc binding in a multi-histidinic peptide fragment.
  Dalton Trans, 39, 1282-1294.  
17194761 E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.McCoy, and G.N.Phillips (2007).
Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.
  Proc Natl Acad Sci U S A, 104, 456-461.
PDB codes: 2gu2 2i3c
16114044 A.Russ, I.Pechik, and N.Andreeva (2005).
Database for three dimensional structures of pepsin-like enzymes using the internal coordinate system.
  Proteins, 61, 223-226.  
15525635 T.Suzuki, K.Ishihara, H.Migaki, W.Matsuura, A.Kohda, K.Okumura, M.Nagao, Y.Yamaguchi-Iwai, and T.Kambe (2005).
Zinc transporters, ZnT5 and ZnT7, are required for the activation of alkaline phosphatases, zinc-requiring enzymes that are glycosylphosphatidylinositol-anchored to the cytoplasmic membrane.
  J Biol Chem, 280, 637-643.  
15377517 V.P.Denisov, J.L.Schlessman, B.García-Moreno E, and B.Halle (2004).
Stabilization of internal charges in a protein: water penetration or conformational change?
  Biophys J, 87, 3982-3994.
PDB code: 1u9r
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.