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PDBsum entry 2zvu

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Oxidoreductase PDB id
2zvu
Jmol
Contents
Protein chain
212 a.a. *
Ligands
VEA
FMT
Waters ×109
* Residue conservation analysis
PDB id:
2zvu
Name: Oxidoreductase
Title: Crystal structure of rat heme oxygenase-1 in complex with ferrous verdoheme
Structure: Heme oxygenase 1. Chain: a. Fragment: unp residues 1-267. Synonym: ho-1, hsp32. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: hmox1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.192     R-free:   0.240
Authors: H.Sato,M.Sugishima,K.Fukuyama,M.Noguchi
Key ref: H.Sato et al. (2009). Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side. Biochem J, 419, 339-345. PubMed id: 19154182 DOI: 10.1042/BJ20082279
Date:
21-Nov-08     Release date:   03-Feb-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06762  (HMOX1_RAT) -  Heme oxygenase 1
Seq:
Struc:
289 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.99.3  - Heme oxygenase (biliverdin-producing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protoheme + 3 AH2 + 3 O2 = biliverdin + Fe2+ + CO + 3 A + 3 H2O
Protoheme
+ 3 × AH(2)
+ 3 × O(2)
=
biliverdin
Bound ligand (Het Group name = VEA)
matches with 95.00% similarity
+ Fe(2+)
+
CO
Bound ligand (Het Group name = FMT)
matches with 66.00% similarity
+ 3 × A
+ 3 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   9 terms 
  Biological process     intracellular signal transduction   40 terms 
  Biochemical function     signal transducer activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1042/BJ20082279 Biochem J 419:339-345 (2009)
PubMed id: 19154182  
 
 
Crystal structure of rat haem oxygenase-1 in complex with ferrous verdohaem: presence of a hydrogen-bond network on the distal side.
H.Sato, M.Sugishima, H.Sakamoto, Y.Higashimoto, C.Shimokawa, K.Fukuyama, G.Palmer, M.Noguchi.
 
  ABSTRACT  
 
HO (haem oxygenase) catalyses the degradation of haem to biliverdin, CO and ferrous iron via three successive oxygenation reactions, i.e. haem to alpha-hydroxyhaem, alpha-hydroxyhaem to alpha-verdohaem and alpha-verdohaem to ferric biliverdin-iron chelate. In the present study, we determined the crystal structure of ferrous alpha-verdohaem-rat HO-1 complex at 2.2 A (1 A=0.1 nm) resolution. The overall structure of the verdohaem complex was similar to that of the haem complex. Water or OH- was co-ordinated to the verdohaem iron as a distal ligand. A hydrogen-bond network consisting of water molecules and several amino acid residues was observed at the distal side of verdohaem. Such a hydrogen-bond network was conserved in the structures of rat HO-1 complexes with haem and with the ferric biliverdin-iron chelate. This hydrogen-bond network may act as a proton donor to form an activated oxygen intermediate, probably a ferric hydroperoxide species, in the degradation of alpha-verdohaem to ferric biliverdin-iron chelate similar to that seen in the first oxygenation step.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19860740 B.Gisk, Y.Yasui, T.Kohchi, and N.Frankenberg-Dinkel (2010).
Characterization of the haem oxygenase protein family in Arabidopsis thaliana reveals a diversity of functions.
  Biochem J, 425, 425-434.  
20502928 J.D.Gardner, L.Yi, S.W.Ragsdale, and T.C.Brunold (2010).
Spectroscopic insights into axial ligation and active-site H-bonding in substrate-bound human heme oxygenase-2.
  J Biol Inorg Chem, 15, 1117-1127.  
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