1IX4

Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of Ferrous and CO-, CN(-)-, and NO-Bound Forms of Rat Heme Oxygenase-1 (HO-1) in Complex with Heme: Structural Implications for Discrimination between CO and O(2) in HO-1.

Sugishima, M.Sakamoto, H.Noguchi, M.Fukuyama, K.

(2003) Biochemistry 42: 9898-9905

  • DOI: 10.1021/bi027268i
  • Primary Citation of Related Structures:  
    1IX3, 1IX4, 1J02, 1UBB

  • PubMed Abstract: 
  • Heme oxygenase (HO) catalyzes heme degradation by utilizing O(2) and reducing equivalents to produce biliverdin IX alpha, iron, and CO. To avoid product inhibition, the heme[bond]HO complex (heme[bond]HO) is structured to markedly increase its affinity for O(2) while suppressing its affinity for CO ...

    Heme oxygenase (HO) catalyzes heme degradation by utilizing O(2) and reducing equivalents to produce biliverdin IX alpha, iron, and CO. To avoid product inhibition, the heme[bond]HO complex (heme[bond]HO) is structured to markedly increase its affinity for O(2) while suppressing its affinity for CO. We determined the crystal structures of rat ferrous heme[bond]HO and heme[bond]HO bound to CO, CN(-), and NO at 2.3, 1.8, 2.0, and 1.7 A resolution, respectively. The heme pocket of ferrous heme-HO has the same conformation as that of the previously determined ferric form, but no ligand is visible on the distal side of the ferrous heme. Fe[bond]CO and Fe[bond]CN(-) are tilted, whereas the Fe[bond]NO is bent. The structure of heme[bond]HO bound to NO is identical to that bound to N(3)(-), which is also bent as in the case of O(2). Notably, in the CO- and CN(-)-bound forms, the heme and its ligands shift toward the alpha-meso carbon, and the distal F-helix shifts in the opposite direction. These shifts allow CO or CN(-) to bind in a tilted fashion without a collision between the distal ligand and Gly139 O and cause disruption of one salt bridge between the heme and basic residue. The structural identity of the ferrous and ferric states of heme[bond]HO indicates that these shifts are not produced on reduction of heme iron. Neither such conformational changes nor a heme shift occurs on NO or N(3)(-) binding. Heme[bond]HO therefore recognizes CO and O(2) by their binding geometries. The marked reduction in the ratio of affinities of CO to O(2) for heme[bond]HO achieved by an increase in O(2) affinity [Migita, C. T., Matera, K. M., Ikeda-Saito, M., Olson, J. S., Fujii, H., Yoshimura, T., Zhou, H., and Yoshida, T. (1998) J. Biol. Chem. 273, 945-949] is explained by hydrogen bonding and polar interactions that are favorable for O(2) binding, as well as by characteristic structural changes in the CO-bound form.


    Related Citations: 
    • Crystal structure of rat heme oxygenase-1 in complex with heme bound to azide. Implication for regiospecific hydroxylation of heme at the alpha-meso carbon.
      Sugishima, M., Sakamoto, H., Higashimoto, Y., Omata, Y., Hayashi, S., Noguchi, M., Fukuyama, K.
      (2003) J Biol Chem 277: 45086

    Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEME OXYGENASE-1A267Rattus norvegicusMutation(s): 0 
Gene Names: Hmox1
EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for P06762 (Rattus norvegicus)
Explore P06762 
Go to UniProtKB:  P06762
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06762
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download Ideal Coordinates CCD File 
C [auth A]CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66α = 90
b = 66β = 90
c = 120.24γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance