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PDBsum entry 2p3x

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protein ligands links
Oxidoreductase PDB id
2p3x
Jmol
Contents
Protein chain
339 a.a. *
Ligands
C2O
Waters ×128
* Residue conservation analysis
PDB id:
2p3x
Name: Oxidoreductase
Title: Crystal structure of grenache (vitis vinifera) polyphenol oxidase
Structure: Polyphenol oxidase, chloroplast. Chain: a. Fragment: polyphenol oxidase. Synonym: ppo, catechol oxidase. Ec: 1.10.3.1
Source: Vitis vinifera. Organism_taxid: 29760. Other_details: grape berries
Resolution:
2.20Å     R-factor:   0.206     R-free:   0.252
Authors: J.P.Reyes Grajeda,V.M.Virador,A.Blanco-Labra,E.Mendiola- Olaya,G.M.Smith,A.Moreno,J.R.Whitaker
Key ref: V.M.Virador et al. (2010). Cloning, sequencing, purification, and crystal structure of Grenache (Vitis vinifera) polyphenol oxidase. J Agric Food Chem, 58, 1189-1201. PubMed id: 20039636 DOI: 10.1021/jf902939q
Date:
09-Mar-07     Release date:   11-Mar-08    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P43311  (PPO_VITVI) -  Polyphenol oxidase, chloroplastic
Seq:
Struc:
 
Seq:
Struc:
607 a.a.
339 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.10.3.1  - Catechol oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O
2 × catechol
+ O(2)
= 2 × 1,2-benzoquinone
+ 2 × H(2)O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1021/jf902939q J Agric Food Chem 58:1189-1201 (2010)
PubMed id: 20039636  
 
 
Cloning, sequencing, purification, and crystal structure of Grenache (Vitis vinifera) polyphenol oxidase.
V.M.Virador, J.P.Reyes Grajeda, A.Blanco-Labra, E.Mendiola-Olaya, G.M.Smith, A.Moreno, J.R.Whitaker.
 
  ABSTRACT  
 
The full-length cDNA sequence (P93622_VITVI) of polyphenol oxidase (PPO) cDNA from grape Vitis vinifera L., cv Grenache, was found to encode a translated protein of 607 amino acids with an expected molecular weight of ca. 67 kDa and a predicted pI of 6.83. The translated amino acid sequence was 99%, identical to that of a white grape berry PPO (1) (5 out of 607 amino acid potential sequence differences). The protein was purified from Grenache grape berries by using traditional methods, and it was crystallized with ammonium acetate by the hanging-drop vapor diffusion method. The crystals were orthorhombic, space group C222(1). The structure was obtained at 2.2 A resolution using synchrotron radiation using the 39 kDa isozyme of sweet potato PPO (PDB code: 1BT1 ) as a phase donor. The basic symmetry of the cell parameters (a, b, and c and alpha, beta, and gamma) as well as in the number of asymmetric units in the unit cell of the crystals of PPO, differed between the two proteins. The structures of the two enzymes are quite similar in overall fold, the location of the helix bundles at the core, and the active site in which three histidines bind each of the two catalytic copper ions, and one of the histidines is engaged in a thioether linkage with a cysteine residue. The possibility that the formation of the Cys-His thioether linkage constitutes the activation step is proposed. No evidence of phosphorylation or glycoslyation was found in the electron density map. The mass of the crystallized protein appears to be only 38.4 kDa, and the processing that occurs in the grape berry that leads to this smaller size is discussed.