1VGI

Crystal structure of xenon bound rat heme-heme oxygenase-1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

CO-trapping site in heme oxygenase revealed by photolysis of its co-bound heme complex: mechanism of escaping from product inhibition

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

(2004) J Mol Biol 341: 7-13

  • DOI: https://doi.org/10.1016/j.jmb.2004.05.048
  • Primary Citation of Related Structures:  
    1ULX, 1VGI

  • PubMed Abstract: 

    Heme oxygenase (HO) catalyzes physiological heme degradation using O(2) and reducing equivalents to produce biliverdin, iron, and CO. Notably, the HO reaction proceeds without product inhibition by CO, which is generated in the conversion reaction of alpha-hydroxyheme to verdoheme, although CO is known to be a potent inhibitor of HO and other heme proteins. In order to probe how endogenous CO is released from the reaction site, we collected X-ray diffraction data from a crystal of the CO-bound form of the ferrous heme-HO complex in the dark and under illumination by a red laser at approximately 35 K. The difference Fourier map indicates that the CO ligand is partially photodissociated from the heme and that the photolyzed CO is trapped in a hydrophobic cavity adjacent to the heme pocket. This hydrophobic cavity was occupied also by xenon, which is similar to CO in terms of size and properties. Taking account of the affinity of CO for the ferrous verdoheme-HO complex being much weaker than that for the ferrous heme complex, the CO derived from alpha-hydroxyheme would be trapped preferentially in the hydrophobic cavity but not coordinated to the iron of verdoheme. This structural device would ensure the smooth progression of the subsequent reaction, from verdoheme to biliverdin, which requires O(2) binding to verdoheme.


  • Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme oxygenase 1267Rattus norvegicusMutation(s): 0 
EC: 1.14.99.3
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.1α = 90
b = 65.1β = 90
c = 120.5γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
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: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description