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PDBsum entry 1wnv

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1wnv
Jmol
Contents
Protein chains
207 a.a. *
Ligands
SO4 ×5
HEM ×3
Waters ×308
* Residue conservation analysis
PDB id:
1wnv
Name: Oxidoreductase
Title: D136a mutant of heme oxygenase from corynebacterium diphtheriae (hmuo)
Structure: Heme oxygenase. Chain: a, b, c. Engineered: yes. Mutation: yes
Source: Corynebacterium diphtheriae. Organism_taxid: 1717. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.85Å     R-factor:   0.168     R-free:   0.204
Authors: T.Matsui,M.Unno,M.Ikeda-Saito
Key ref:
T.Matsui et al. (2005). Roles of distal Asp in heme oxygenase from Corynebacterium diphtheriae, HmuO: A water-driven oxygen activation mechanism. J Biol Chem, 280, 2981-2989. PubMed id: 15528205 DOI: 10.1074/jbc.M410263200
Date:
10-Aug-04     Release date:   09-Nov-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71119  (HMUO_CORDI) -  Heme oxygenase
Seq:
Struc:
215 a.a.
207 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M410263200 J Biol Chem 280:2981-2989 (2005)
PubMed id: 15528205  
 
 
Roles of distal Asp in heme oxygenase from Corynebacterium diphtheriae, HmuO: A water-driven oxygen activation mechanism.
T.Matsui, M.Furukawa, M.Unno, T.Tomita, M.Ikeda-Saito.
 
  ABSTRACT  
 
Heme oxygenases found in mammals, plants, and bacteria catalyze degradation of heme using the same mechanism. Roles of distal Asp (Asp-136) residue in HmuO, a heme oxygenase of Corynebacterium diphtheriae, have been investigated by site-directed mutagenesis, enzyme kinetics, resonance Raman spectroscopy, and x-ray crystallography. Replacements of the Asp-136 by Ala and Phe resulted in reduced heme degradation activity due to the formation of ferryl heme, showing that the distal Asp is critical in HmuO heme oxygenase activity. D136N HmuO catalyzed heme degradation at a similar efficiency to wild type and D136E HmuO, implying that the carboxylate moiety is not required for the heme catabolism by HmuO. Resonance Raman results suggest that the inactive ferryl heme formation in the HmuO mutants is induced by disruption of the interaction between a reactive Fe-OOH species and an adjacent distal pocket water molecule. Crystal structural analysis of the HmuO mutants confirms partial disappearance of this nearby water in D136A HmuO. Our results provide the first experimental evidence for the catalytic importance of the nearby water molecule that can be universally critical in heme oxygenase catalysis and propose that the distal Asp helps in positioning the key water molecule at a position suitable for efficient activation of the Fe-OOH species.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Reaction intermediates in the heme degradation by heme oxygenase.
Figure 6.
FIG. 6. Active site structures of the ferric heme complex of wild type (a), D136E (b), D136N (c), and D136A HmuO (d). Red and yellow balls are water and iodide ions, respectively. Broken lines indicate H-bonding interactions.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 2981-2989) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19842713 D.Peng, H.Ogura, W.Zhu, L.H.Ma, J.P.Evans, P.R.Ortiz de Montellano, and G.N.La Mar (2009).
Coupling of the distal hydrogen bond network to the exogenous ligand in substrate-bound, resting state human heme oxygenase.
  Biochemistry, 48, 11231-11242.  
19243105 H.Ogura, J.P.Evans, D.Peng, J.D.Satterlee, P.R.Ortiz de Montellano, and G.N.La Mar (2009).
The orbital ground state of the azide-substrate complex of human heme oxygenase is an indicator of distal H-bonding: implications for the enzyme mechanism.
  Biochemistry, 48, 3127-3137.  
18976815 L.H.Ma, Y.Liu, X.Zhang, T.Yoshida, and G.N.La Mar (2009).
1H NMR study of the effect of variable ligand on heme oxygenase electronic and molecular structure.
  J Inorg Biochem, 103, 10-19.  
17534530 M.Unno, T.Matsui, and M.Ikeda-Saito (2007).
Structure and catalytic mechanism of heme oxygenase.
  Nat Prod Rep, 24, 553-570.  
17263425 R.Garcia-Serres, R.M.Davydov, T.Matsui, M.Ikeda-Saito, B.M.Hoffman, and B.H.Huynh (2007).
Distinct reaction pathways followed upon reduction of oxy-heme oxygenase and oxy-myoglobin as characterized by Mössbauer spectroscopy.
  J Am Chem Soc, 129, 1402-1412.  
16900547 Y.Lu (2006).
Biosynthetic inorganic chemistry.
  Angew Chem Int Ed Engl, 45, 5588-5601.  
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.