PDBsum entry 2e7e

Oxidoreductase

PDB id: 2e7e

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

Protein chain

P06762  (HMOX1_RAT) -  Heme oxygenase 1 from Rattus norvegicus

Seq: 289 a.a.

Struc: 212 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.14.18 - heme oxygenase (biliverdin-producing).
• Reaction: heme b + 3 reduced [NADPH--hemoprotein reductase] + 3 O2 = biliverdin IXalpha + CO + Fe²⁺ + 3 oxidized [NADPH--hemoprotein reductase] + 3 H2O + H⁺

heme b (Bound ligand (Het Group name = HEM) matches with 95.45% similarity) + 3 × reduced [NADPH--hemoprotein reductase] + 3 × O2 = biliverdin IXalpha + CO + Fe(2+) + 3 × oxidized [NADPH--hemoprotein reductase] + 3 × H2O + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.