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PDBsum entry 1iw1

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1iw1
Jmol
Contents
Protein chains
212 a.a. *
Ligands
SUC
SO4 ×10
HEM ×3
Waters ×584
* Residue conservation analysis
PDB id:
1iw1
Name: Oxidoreductase
Title: Crystal structure of a heme oxygenase (hmuo) from corynebacterium diphtheriae complexed with heme in the ferrous state
Structure: Heme oxygenase. Chain: a, b, c. Engineered: yes
Source: Corynebacterium diphtheriae. Organism_taxid: 1717. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.50Å     R-factor:   0.178     R-free:   0.202
Authors: S.Hirotsu,M.Unno,G.C.Chu,D.S.Lee,S.Y.Park,Y.Shiro,M.Ikeda- Saito,Riken Structural Genomics/proteomics Initiative (Rsgi
Key ref:
S.Hirotsu et al. (2004). The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae. J Biol Chem, 279, 11937-11947. PubMed id: 14645223 DOI: 10.1074/jbc.M311631200
Date:
04-Apr-02     Release date:   04-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71119  (HMUO_CORDI) -  Heme oxygenase
Seq:
Struc:
215 a.a.
212 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)
= 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.M311631200 J Biol Chem 279:11937-11947 (2004)
PubMed id: 14645223  
 
 
The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae.
S.Hirotsu, G.C.Chu, M.Unno, D.S.Lee, T.Yoshida, S.Y.Park, Y.Shiro, M.Ikeda-Saito.
 
  ABSTRACT  
 
Crystal structures of the ferric and ferrous heme complexes of HmuO, a 24-kDa heme oxygenase of Corynebacterium diphtheriae, have been refined to 1.4 and 1.5 A resolution, respectively. The HmuO structures show that the heme group is closely sandwiched between the proximal and distal helices. The imidazole group of His-20 is the proximal heme ligand, which closely eclipses the beta- and delta-meso axis of the porphyrin ring. A long range hydrogen bonding network is present, connecting the iron-bound water ligand to the solvent water molecule. This enables proton transfer from the solvent to the catalytic site, where the oxygen activation occurs. In comparison to the ferric complex, the proximal and distal helices move closer to the heme plane in the ferrous complex. Together with the kinked distal helix, this movement leaves only the alpha-meso carbon atom accessible to the iron-bound dioxygen. The heme pocket architecture is responsible for stabilization of the ferric hydroperoxo-active intermediate by preventing premature heterolytic O-O bond cleavage. This allows the enzyme to oxygenate selectively at the alpha-meso carbon in HmuO catalysis.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. Conformations of the proximal and distal helices. A, superimposition of the structures of the proximal and distal helices in three HmuO molecules in the asymmetric unit is shown. Three molecules are individually colored red, blue, and green. Heme is also shown by ball-and-stick models. B, superimposition of two human HO-1 molecules (Protein Data Bank code 1N45 [PDB] ) in the asymmetric unit is shown. The molecule with open conformation is colored blue and closed conformation red. For both A and B, a close up view representing hydrophobic interactions between the C-terminal regions of the proximal and distal helices are shown in the right-hand panel.
Figure 6.
FIG. 6. Structures representing the extended hydrogen bonding network. A, hydrogen bonding network involved in proton pathway is shown by ball-and-stick models. Water molecules are represented by pink spheres and are numbered from W1 to W7 in order of their distances from heme iron. Dotted lines represent hydrogen-bonding contacts, and numbers beside them represent their length in Å. B, HmuO residues and water molecules contributing to the formation of the hydrogen bonding network are emphasized within the overall structure represented by blue stick model. An accessible surface around Asp-86 is also shown above. Blue corresponds to positive and red to negative potentials.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 11937-11947) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20356038 B.R.Streit, B.Blanc, G.S.Lukat-Rodgers, K.R.Rodgers, and J.L.DuBois (2010).
How active-site protonation state influences the reactivity and ligation of the heme in chlorite dismutase.
  J Am Chem Soc, 132, 5711-5724.  
20378668 G.S.Shekhawat, and K.Verma (2010).
Haem oxygenase (HO): an overlooked enzyme of plant metabolism and defence.
  J Exp Bot, 61, 2255-2270.  
20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
Heme proteins--diversity in structural characteristics, function, and folding.
  Proteins, 78, 2349-2368.  
19917297 N.Chim, A.Iniguez, T.Q.Nguyen, and C.W.Goulding (2010).
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis.
  J Mol Biol, 395, 595-608.
PDB code: 3hx9
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.  
17322319 C.A.Kunkle, and M.P.Schmitt (2007).
Comparative analysis of hmuO function and expression in Corynebacterium species.
  J Bacteriol, 189, 3650-3654.  
17965015 C.M.Bianchetti, L.Yi, S.W.Ragsdale, and G.N.Phillips (2007).
Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2.
  J Biol Chem, 282, 37624-37631.
PDB codes: 2q32 2qpp 2rgz
17534530 M.Unno, T.Matsui, and M.Ikeda-Saito (2007).
Structure and catalytic mechanism of heme oxygenase.
  Nat Prod Rep, 24, 553-570.  
16428411 E.P.Skaar, A.H.Gaspar, and O.Schneewind (2006).
Bacillus anthracis IsdG, a heme-degrading monooxygenase.
  J Bacteriol, 188, 1071-1080.  
16774589 G.Rudolph, H.Hennecke, and H.M.Fischer (2006).
Beyond the Fur paradigm: iron-controlled gene expression in rhizobia.
  FEMS Microbiol Rev, 30, 631-648.  
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.  
16817889 P.J.Linley, M.Landsberger, T.Kohchi, J.B.Cooper, and M.J.Terry (2006).
The molecular basis of heme oxygenase deficiency in the pcd1 mutant of pea.
  FEBS J, 273, 2594-2606.  
16952937 S.Puri, and M.R.O'Brian (2006).
The hmuQ and hmuD genes from Bradyrhizobium japonicum encode heme-degrading enzymes.
  J Bacteriol, 188, 6476-6482.  
17076701 T.Gohya, X.Zhang, T.Yoshida, and C.T.Migita (2006).
Spectroscopic characterization of a higher plant heme oxygenase isoform-1 from Glycine max (soybean)--coordination structure of the heme complex and catabolism of heme.
  FEBS J, 273, 5384-5399.  
16769893 T.Ueno, N.Yokoi, M.Unno, T.Matsui, Y.Tokita, M.Yamada, M.Ikeda-Saito, H.Nakajima, and Y.Watanabe (2006).
Design of metal cofactors activated by a protein-protein electron transfer system.
  Proc Natl Acad Sci U S A, 103, 9416-9421.
PDB codes: 1wzd 1wzf 1wzg
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.  
16275907 M.D.Suits, G.P.Pal, K.Nakatsu, A.Matte, M.Cygler, and Z.Jia (2005).
Identification of an Escherichia coli O157:H7 heme oxygenase with tandem functional repeats.
  Proc Natl Acad Sci U S A, 102, 16955-16960.
PDB code: 1u9t
15487950 C.Wandersman, and P.Delepelaire (2004).
Bacterial iron sources: from siderophores to hemophores.
  Annu Rev Microbiol, 58, 611-647.  
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
  15345142 N.Frankenberg-Dinkel (2004).
Bacterial heme oxygenases.
  Antioxid Redox Signal, 6, 825-834.  
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 code is shown on the right.