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PDBsum entry 3hb6

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protein ligands links
Oxidoreductase PDB id
3hb6
Jmol
Contents
Protein chain
476 a.a. *
Ligands
HEM
SO4 ×8
GOL
Waters ×476
* Residue conservation analysis
PDB id:
3hb6
Name: Oxidoreductase
Title: Inactive mutant h54f of proteus mirabilis catalase
Structure: Catalase. Chain: a. Engineered: yes. Mutation: yes
Source: Proteus mirabilis. Organism_taxid: 584. Gene: kata. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.203     R-free:   0.236
Authors: P.Andeoletti,H.M.Jouve,P.Gouet
Key ref: P.Andreoletti et al. (2009). Verdoheme formation in Proteus mirabilis catalase. Biochim Biophys Acta, 1790, 741-753. PubMed id: 19394409 DOI: 10.1016/j.bbagen.2009.04.010
Date:
04-May-09     Release date:   12-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42321  (CATA_PROMI) -  Catalase
Seq:
Struc:
484 a.a.
476 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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)
= O(2)
+ 2 × H(2)O
      Cofactor: Heme; Mn(2+)
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.bbagen.2009.04.010 Biochim Biophys Acta 1790:741-753 (2009)
PubMed id: 19394409  
 
 
Verdoheme formation in Proteus mirabilis catalase.
P.Andreoletti, J.M.Mouesca, P.Gouet, M.Jaquinod, C.Capeillère-Blandin, H.M.Jouve.
 
  ABSTRACT  
 
BACKGROUND: Heme oxidative degradation has been extensively investigated in peroxidases but not in catalases. The verdoheme formation, a product of heme oxidation which inactivates the enzyme, was studied in Proteus mirabilis catalase. METHODS: The verdoheme was generated by adding peracetic acid and analyzed by mass spectrometry and spectrophotometry. RESULTS: Kinetics follow-up of different catalase reactional intermediates shows that i) the formation of compound I always precedes that of verdoheme, ii) compound III is never observed, iii) the rate of compound II decomposition is not compatible with that of verdoheme formation, and iv) dithiothreitol prevents the verdoheme formation but not that of compound II, whereas NADPH prevents both of them. The formation of verdoheme is strongly inhibited by EDTA but not increased by Fe3+ or Cu2+ salts. The generation of verdoheme is facilitated by the presence of protein radicals as observed in the F194Y mutated catalase. The inability of the inactive variant (H54F) to form verdoheme, indicates that the heme oxidation is fully associated to the enzyme catalysis. CONCLUSION: These data, taken together, strongly suggest that the verdoheme formation pathway originates from compound I rather than from compound II. GENERAL SIGNIFICANCE: The autocatalytic verdoheme formation is likely to occur in vivo.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20716293 D.E.Heck, M.Shakarjian, H.D.Kim, J.D.Laskin, and A.M.Vetrano (2010).
Mechanisms of oxidant generation by catalase.
  Ann N Y Acad Sci, 1203, 120-125.  
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