spacer
spacer

PDBsum entry 2iuf

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2iuf
Jmol
Contents
Protein chains
688 a.a. *
Ligands
HDD ×2
NAG ×5
__O ×2
ACT ×13
F50 ×3
MPD
NAG-NAG
Metals
_CA ×6
Waters ×1490
* Residue conservation analysis
PDB id:
2iuf
Name: Oxidoreductase
Title: The structures of penicillium vitale catalase: resting state, oxidised state (compound i) and complex with aminotriazole
Structure: Catalase. Chain: a, e. Ec: 1.11.1.6
Source: Penicillium janthinellum. Organism_taxid: 5079
Biol. unit: Tetramer (from PDB file)
Resolution:
1.71Å     R-factor:   0.131     R-free:   0.154
Authors: G.Murshudov,A.Borovik,A.Grebenko,V.Barynin,A.Vagin, W.Melik- Adamyan
Key ref: M.Alfonso-Prieto et al. (2007). The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations. J Am Chem Soc, 129, 4193-4205. PubMed id: 17358056 DOI: 10.1021/ja063660y
Date:
02-Jun-06     Release date:   10-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
D9N167  (D9N167_PENJA) -  Catalase
Seq:
Struc:
 
Seq:
Struc:
688 a.a.
689 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.6  - Catalase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2O2 = O2 + 2 H2O
2 × H(2)O(2)
Bound ligand (Het Group name = F50)
matches with 40.00% similarity
= O(2)
+ 2 × H(2)O
      Cofactor: Heme; Mn(2+)
Heme
Bound ligand (Het Group name = HDD) matches with 93.00% similarity
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/ja063660y J Am Chem Soc 129:4193-4205 (2007)
PubMed id: 17358056  
 
 
The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations.
M.Alfonso-Prieto, A.Borovik, X.Carpena, G.Murshudov, W.Melik-Adamyan, I.Fita, C.Rovira, P.C.Loewen.
 
  ABSTRACT  
 
The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
17419051 M.Dal Peraro, P.Ruggerone, S.Raugei, F.L.Gervasio, and P.Carloni (2007).
Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.
  Curr Opin Struct Biol, 17, 149-156.  
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.