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PDBsum entry 3i9t

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protein ligands links
Oxidoreductase PDB id
3i9t
Jmol
Contents
Protein chain
212 a.a. *
Ligands
HEM-DTV
Waters ×135
* Residue conservation analysis
PDB id:
3i9t
Name: Oxidoreductase
Title: Crystal structure of the rat heme oxygenase (ho-1) in comple heme binding dithiothreitol (dtt)
Structure: Heme oxygenase 1. Chain: a. Fragment: unp residues 1-261. Synonym: ho-1, hsp32. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: hmox1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.165     R-free:   0.209
Authors: T.Matsui,M.Unno,M.Ikeda-Saito
Key ref: T.Matsui et al. (2010). Dioxygen activation for the self-degradation of heme: reaction mechanism and regulation of heme oxygenase. Inorg Chem, 49, 3602-3609. PubMed id: 20380462 DOI: 10.1021/ic901869t
Date:
13-Jul-09     Release date:   19-May-10    
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
Bound ligand (Het Group name = HEM)
matches with 95.00% similarity
+ 3 × AH(2)
+ 3 × O(2)
= biliverdin
+ Fe(2+)
+ CO
+ 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: 10.1021/ic901869t Inorg Chem 49:3602-3609 (2010)
PubMed id: 20380462  
 
 
Dioxygen activation for the self-degradation of heme: reaction mechanism and regulation of heme oxygenase.
T.Matsui, M.Iwasaki, R.Sugiyama, M.Unno, M.Ikeda-Saito.
 
  ABSTRACT  
 
Heme oxygenase (HO) catalyzes the regiospecific conversion of heme to biliverdin, CO, and free iron through three successive oxygenation reactions. HO catalysis is unique in that all three O(2) activations are performed by the substrate itself. This Forum Article overviews our current understanding on the structural and biochemical properties of HO catalysis, especially its first and third oxygenation steps. The HO first step, regiospecific hydroxylation of the porphyrin alpha-meso-carbon atom, is of particular interest because of its sharp contrast to O(2) activation by cytochrome P450. HO was proposed to utilize the FeOOH species but not conventional ferryl hemes as a reactive intermediate for self-hydroxylation. We have succeeded in preparing and characterizing the FeOOH species of HO at low temperature, and our analyses of its reaction, together with mutational and crystallographic studies, reveal that protonation of FeOOH by a distal water molecule is critical in promoting the unique self-hydroxylation. The second oxygenation is a rapid, spontaneous autooxidation of the reactive alpha-meso-hydroxyheme in which the HO enzyme does not play a critical role. Further O(2) activation by verdoheme cleaves its porphyrin macrocycle to form biliverdin and free ferrous iron. This third step has been considered to be a major rate-determining step of HO catalysis to regulate the enzyme activity. Our reaction analysis strongly supports the FeOOH verdoheme as the key intermediate of the ring-opening reaction. This mechanism is very similar to that of the first meso-hydroxylation, and the distal water is suggested to enhance the third step as expected from the similarity. The HO mechanistic studies highlight the catalytic importance of the distal hydrogen-bonding network, and this manuscript also involves our attempts to develop HO inhibitors targeting the unique distal structure.