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PDBsum entry 2rgz

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2rgz
Jmol
Contents
Protein chains
214 a.a. *
Ligands
HEM ×2
Waters ×83
* Residue conservation analysis
PDB id:
2rgz
Name: Oxidoreductase
Title: Ensemble refinement of the protein crystal structure of huma oxygenase-2 c127a (ho-2) with bound heme
Structure: Heme oxygenase 2. Chain: a, b. Synonym: ho-2. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hmox2, ho2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.61Å     R-factor:   0.161     R-free:   0.249
Ensemble: 16 models
Authors: C.M.Bianchetti,C.A.Bingman,E.Bitto,G.E.Wesenberg,G.N.Phillip Center For Eukaryotic Structural Genomics (Cesg)
Key ref:
C.M.Bianchetti et al. (2007). Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2. J Biol Chem, 282, 37624-37631. PubMed id: 17965015 DOI: 10.1074/jbc.M707396200
Date:
05-Oct-07     Release date:   23-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P30519  (HMOX2_HUMAN) -  Heme oxygenase 2
Seq:
Struc:
316 a.a.
214 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 95.45% 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     heme oxygenase (decyclizing) activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M707396200 J Biol Chem 282:37624-37631 (2007)
PubMed id: 17965015  
 
 
Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2.
C.M.Bianchetti, L.Yi, S.W.Ragsdale, G.N.Phillips.
 
  ABSTRACT  
 
Heme oxygenase (HO) catalyzes the first step in the heme degradation pathway. The crystal structures of apo- and heme-bound truncated human HO-2 reveal a primarily alpha-helical architecture similar to that of human HO-1 and other known HOs. Proper orientation of heme in HO-2 is required for the regioselective oxidation of the alpha-mesocarbon. This is accomplished by interactions within the heme binding pocket, which is made up of two helices. The iron coordinating residue, His(45), resides on the proximal helix. The distal helix contains highly conserved glycine residues that allow the helix to flex and interact with the bound heme. Tyr(154), Lys(199), and Arg(203) orient the heme through direct interactions with the heme propionates. The rearrangements of side chains in heme-bound HO-2 compared with apoHO-2 further elucidate HO-2 heme interactions.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Schematic of the overall reaction catalyzed by heme oxygenase.
Figure 5.
FIGURE 5. Electron density maps of apo- and heme-bound HO-2. A, stereo view of the F[o] - F[c] map of the heme-bound HO-2 heme pocket contoured at 3 . The heme group is shown with carbon in gray, oxygen in red, and iron in orange. The red spheres represent water molecules. B, stereo view of the 2 F[o] - F[c] of the hydrophobic region in the heme pocket of apoHO-2 shown at 1 . The Triton X-100 is shown with carbon in yellow and oxygen in red.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 37624-37631) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20812781 S.W.Ragsdale, and L.Yi (2011).
Thiol/Disulfide redox switches in the regulation of heme binding to proteins.
  Antioxid Redox Signal, 14, 1039-1047.  
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.  
20555417 D.Vukomanovic, B.McLaughlin, M.N.Rahman, J.Z.Vlahakis, G.Roman, R.A.Dercho, R.T.Kinobe, M.Hum, J.F.Brien, Z.Jia, W.A.Szarek, and K.Nakatsu (2010).
Recombinant truncated and microsomal heme oxygenase-1 and -2: differential sensitivity to inhibitors.
  Can J Physiol Pharmacol, 88, 480-486.  
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.  
19694439 J.P.Evans, S.Kandel, and P.R.Ortiz de Montellano (2009).
Isocyanides inhibit human heme oxygenases at the verdoheme stage.
  Biochemistry, 48, 8920-8928.  
19473966 L.Yi, P.M.Jenkins, L.I.Leichert, U.Jakob, J.R.Martens, and S.W.Ragsdale (2009).
Heme regulatory motifs in heme oxygenase-2 form a thiol/disulfide redox switch that responds to the cellular redox state.
  J Biol Chem, 284, 20556-20561.  
  20981135 M.R.Nourani, S.Yazdani, M.H.Roudkenar, M.Ebrahimi, R.Halabian, L.Mirbagheri, M.Ghanei, and A.A.Fooladi (2009).
HO1 mRNA and Protein do not Change in Parallel in Bronchial Biopsies of Patients After Long Term Exposure to Sulfur Mustard.
  Gene Regul Syst Bio, 4, 83-90.  
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.