spacer
spacer

PDBsum entry 1v8x

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1v8x
Jmol
Contents
Protein chains
210 a.a. *
Ligands
SUC
SO4 ×12
HEM-OXY ×3
Waters ×449
* Residue conservation analysis
PDB id:
1v8x
Name: Oxidoreductase
Title: Crystal structure of the dioxygen-bound heme oxygenase from corynebacterium diphtheriae
Structure: Heme oxygenase. Chain: a, b, c. Engineered: yes
Source: Corynebacterium diphtheriae. Organism_taxid: 1717. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.85Å     R-factor:   0.157     R-free:   0.193
Authors: M.Unno,T.Matsui,G.C.Chu,M.Couture,T.Yoshida,D.L.Rousseau, J.S.Olson,M.Ikeda-Saito
Key ref:
M.Unno et al. (2004). Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae: implications for heme oxygenase function. J Biol Chem, 279, 21055-21061. PubMed id: 14966119 DOI: 10.1074/jbc.M400491200
Date:
15-Jan-04     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71119  (HMUO_CORDI) -  Heme oxygenase
Seq:
Struc:
215 a.a.
210 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.1.14.99.3  - 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)
Bound ligand (Het Group name = OXY)
corresponds exactly
= 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.M400491200 J Biol Chem 279:21055-21061 (2004)
PubMed id: 14966119  
 
 
Crystal structure of the dioxygen-bound heme oxygenase from Corynebacterium diphtheriae: implications for heme oxygenase function.
M.Unno, T.Matsui, G.C.Chu, M.Couture, T.Yoshida, D.L.Rousseau, J.S.Olson, M.Ikeda-Saito.
 
  ABSTRACT  
 
HmuO, a heme oxygenase of Corynebacterium diphtheriae, catalyzes degradation of heme using the same mechanism as the mammalian enzyme. The oxy form of HmuO, the precursor of the catalytically active ferric hydroperoxo species, has been characterized by ligand binding kinetics, resonance Raman spectroscopy, and x-ray crystallography. The oxygen association and dissociation rate constants are 5 microm(-1) s(-1) and 0.22 s(-1), respectively, yielding an O(2) affinity of 21 microm(-1), which is approximately 20 times greater than that of mammalian myoglobins. However, the affinity of HmuO for CO is only 3-4-fold greater than that for mammalian myoglobins, implying the presence of strong hydrogen bonding interactions in the distal pocket of HmuO that preferentially favor O(2) binding. Resonance Raman spectra show that the Fe-O(2) vibrations are tightly coupled to porphyrin vibrations, indicating the highly bent Fe-O-O geometry that is characteristic of the oxy forms of heme oxygenases. In the crystal structure of the oxy form the Fe-O-O angle is 110 degrees, the O-O bond is pointed toward the heme alpha-meso-carbon by direct steric interactions with Gly-135 and Gly-139, and hydrogen bonds occur between the bound O(2) and the amide nitrogen of Gly-139 and a distal pocket water molecule, which is a part of an extended hydrogen bonding network that provides the solvent protons required for oxygen activation. In addition, the O-O bond is orthogonal to the plane of the proximal imidazole side chain, which facilitates hydroxylation of the porphyrin alpha-meso-carbon by preventing premature O-O bond cleavage.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Schematics of heme oxygenase catalytic intermediates.
Figure 3.
FIG. 3. Structure of the oxygen binding site. The final [A]-weighted 2F[o] - F[c] map (blue) at the 1.8 level and the simulated annealing omit F[o] - F[c] map (red) at the 4.2 level. Water molecules are represented by W plus a number, and D, G, and Q are standard single letter amino acid abbreviations with position numbers.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 21055-21061) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21351297 E.Olsson, A.Martinez, K.Teigen, and V.R.Jensen (2011).
Formation of the iron-oxo hydroxylating species in the catalytic cycle of aromatic amino acid hydroxylases.
  Chemistry, 17, 3746-3758.  
19939208 M.Kajimura, R.Fukuda, R.M.Bateman, T.Yamamoto, and M.Suematsu (2010).
Interactions of multiple gas-transducing systems: hallmarks and uncertainties of CO, NO, and H2S gas biology.
  Antioxid Redox Signal, 13, 157-192.  
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.  
19082087 R.L.Shook, and A.S.Borovik (2008).
The effects of hydrogen bonds on metal-mediated O2 activation and related processes.
  Chem Commun (Camb), (), 6095-6107.  
18713745 W.C.Lee, M.L.Reniere, E.P.Skaar, and M.E.Murphy (2008).
Ruffling of metalloporphyrins bound to IsdG and IsdI, two heme-degrading enzymes in Staphylococcus aureus.
  J Biol Chem, 283, 30957-30963.
PDB codes: 2zdo 2zdp
17197414 F.Forouhar, J.L.Anderson, C.G.Mowat, S.M.Vorobiev, A.Hussain, M.Abashidze, C.Bruckmann, S.J.Thackray, J.Seetharaman, T.Tucker, R.Xiao, L.C.Ma, L.Zhao, T.B.Acton, G.T.Montelione, S.K.Chapman, and L.Tong (2007).
Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase.
  Proc Natl Acad Sci U S A, 104, 473-478.
PDB codes: 2nw7 2nw8 2nw9 2nwb
  18379640 I.G.Denisov, D.C.Victoria, and S.G.Sligar (2007).
Cryoradiolytic reduction of heme proteins: Maximizing dose dependent yield.
  Radiat Phys Chem Oxf Engl 1993, 76, 714-721.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
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.  
16804678 H.Li, J.Igarashi, J.Jamal, W.Yang, and T.L.Poulos (2006).
Structural studies of constitutive nitric oxide synthases with diatomic ligands bound.
  J Biol Inorg Chem, 11, 753-768.
PDB codes: 2g6h 2g6i 2g6j 2g6k 2g6l 2g6m 2g6n 2g6o
16388581 J.Wang, J.P.Evans, H.Ogura, G.N.La Mar, and P.R.Ortiz de Montellano (2006).
Alteration of the regiospecificity of human heme oxygenase-1 by unseating of the heme but not disruption of the distal hydrogen bonding network.
  Biochemistry, 45, 61-73.  
16704267 L.H.Ma, Y.Liu, X.Zhang, T.Yoshida, and G.N.La Mar (2006).
1H NMR study of the magnetic properties and electronic structure of the hydroxide complex of substrate-bound heme oxygenase from Neisseria meningitidis: influence of the axial water deprotonation on the distal H-bond network.
  J Am Chem Soc, 128, 6657-6668.  
16683803 L.H.Ma, Y.Liu, X.Zhang, T.Yoshida, K.C.Langry, K.M.Smith, and G.N.La Mar (2006).
Modulation of the axial water hydrogen-bonding properties by chemical modification of the substrate in resting state, substrate-bound heme oxygenase from Neisseria meningitidis; coupling to the distal H-bond network via ordered water molecules.
  J Am Chem Soc, 128, 6391-6399.  
16548515 Y.Liu, L.H.Ma, X.Zhang, T.Yoshida, J.D.Satterlee, and G.N.La Mar (2006).
Characterization of the spontaneous "aging" of the heme oxygenase from the pathological bacterium Neisseria meningitidis via cleavage of the C-terminus in contact with the substrate. Implications for functional studies and the crystal structure.
  Biochemistry, 45, 3875-3886.  
15690204 L.Lad, A.Koshkin, P.R.de Montellano, and T.L.Poulos (2005).
Crystal structures of the G139A, G139A-NO and G143H mutants of human heme oxygenase-1. A finely tuned hydrogen-bonding network controls oxygenase versus peroxidase activity.
  J Biol Inorg Chem, 10, 138-146.
PDB codes: 1xjz 1xk0 1xk1
15520015 R.Wu, E.P.Skaar, R.Zhang, G.Joachimiak, P.Gornicki, O.Schneewind, and A.Joachimiak (2005).
Staphylococcus aureus IsdG and IsdI, heme-degrading enzymes with structural similarity to monooxygenases.
  J Biol Chem, 280, 2840-2846.
PDB codes: 1sqe 1xbw
15560792 M.Sugishima, C.T.Migita, X.Zhang, T.Yoshida, and K.Fukuyama (2004).
Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme.
  Eur J Biochem, 271, 4517-4525.
PDB code: 1we1
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.