spacer
spacer

PDBsum entry 2e7e

Go to PDB code: 
protein ligands links
Oxidoreductase PDB id
2e7e
Jmol
Contents
Protein chain
212 a.a. *
Ligands
CYN-HEM
Waters ×182
* Residue conservation analysis
PDB id:
2e7e
Name: Oxidoreductase
Title: Bent-binding of cyanide to the heme iron in rat heme oxygenase-1
Structure: Heme oxygenase 1. Chain: a. Fragment: soluble fragment. Synonym: ho-1, hsp32. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.194     R-free:   0.218
Authors: M.Sugishima,K.Fukuyama
Key ref:
M.Sugishima et al. (2007). Alternative cyanide-binding modes to the haem iron in haem oxygenase. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 471-474. PubMed id: 17554165 DOI: 10.1107/S174430910702475X
Date:
09-Jan-07     Release date:   19-Jun-07    
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: 10.1107/S174430910702475X Acta Crystallogr Sect F Struct Biol Cryst Commun 63:471-474 (2007)
PubMed id: 17554165  
 
 
Alternative cyanide-binding modes to the haem iron in haem oxygenase.
M.Sugishima, K.Oda, T.Ogura, H.Sakamoto, M.Noguchi, K.Fukuyama.
 
  ABSTRACT  
 
Cyanide is a well known potent inhibitor of haem proteins, including haem oxygenase (HO). Generally, cyanide coordinates to the ferric haem iron with a linear binding geometry; the Fe-C-N angle ranges from 160 to 180 degrees . The Fe-C-N angle observed in the crystal structure of haem-HO bound to cyanide prepared at alkaline pH was 166 degrees . Here, it is reported that cyanide can bind to the haem iron in HO in a bent mode when the ternary complex is prepared at neutral pH; a crystal structure showed that the Fe-C-N angle was bent by 47 degrees . Unlike the ternary complex prepared at alkaline pH, in which the haem group, including the proximal ligand and the distal helix, was displaced upon cyanide binding, the positions of the haem group and the distal helix in the complex prepared at neutral pH were nearly identical to those in haem-HO. Cyanide that was bound to haem-HO with a bent geometry was readily photodissociated, whereas that bound with a linear geometry was not photodissociated. Thus, alternative cyanide-binding modes with linear and bent geometries exist in the crystalline state of haem-HO.
 
  Selected figure(s)  
 
Figure 2.
Superimposition of haem --HO (green; Sugishima et al., 2003[triangle]), CN^[minus sign] --haem --HO (yellow, pH 6.8) and CN^[minus sign] --haem --HO (blue, pH 9.7). Except for the proximal histidine, only the C^[alpha] traces are shown for clarity. The crystal structures of CN^[minus sign] --haem --HO at pH 6.8 and pH 9.7 were superimposed on the structure of haem --HO so as to minimize the r.m.s. deviations of C^[alpha] atoms. Following the distal helix is the G-helix, which contains the basic residues (Lys179 and Arg183) involved in the salt bridges to haem propionates. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 June 1; 63(Pt 6): 471–474. Published online 2007 May 31. doi: 10.1107/S174430910702475X. Copyright [copyright] International Union of Crystallography 2007
Figure 3.
Photodissociation of cyanide. A difference Fourier map calculated between data sets obtained in the dark and under continuous illumination from a red laser is superimposed on the ball-and-stick model around the haem group. Blue and red indicate newly appeared and the diminished densities, respectively (contoured at [plus minus]3[sigma]). (a) 5 mM KCN pH 6.8. (b) 50 mM KCN pH 9.7. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 June 1; 63(Pt 6): 471–474. Published online 2007 May 31. doi: 10.1107/S174430910702475X. Copyright [copyright] International Union of Crystallography 2007
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2007, 63, 471-474) copyright 2007.  
  Figures were selected by an automated process.