Cytochrome c prime from alcaligenes xylosoxidans: carbon monooxide bound L16G variant at 1.05 A resolution: unrestraint refinement

Experimental Data Snapshot

  • Resolution: 1.05 Å

Starting Model: experimental
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Carbon Monoxide Poisoning is Prevented by the Energy Costs of Conformational Changes in Gas- Binding Haemproteins.

Antonyuk, S.V.Rustage, N.Petersen, C.A.Arnst, J.L.Heyes, D.J.Sharma, R.Berry, N.G.Scrutton, N.S.Eady, R.R.Andrew, C.R.Hasnain, S.S.

(2011) Proc Natl Acad Sci U S A 108: 15780

  • DOI: https://doi.org/10.1073/pnas.1109051108
  • Primary Citation of Related Structures:  
    2YKZ, 2YL0, 2YL1, 2YL3, 2YL7, 2YLD, 2YLG, 2YLI, 3ZQV, 3ZQY, 3ZTM, 3ZTZ, 3ZWI

  • PubMed Abstract: 

    Carbon monoxide (CO) is a product of haem metabolism and organisms must evolve strategies to prevent endogenous CO poisoning of haemoproteins. We show that energy costs associated with conformational changes play a key role in preventing irreversible CO binding. AxCYTcp is a member of a family of haem proteins that form stable 5c-NO and 6c-CO complexes but do not form O(2) complexes. Structure of the AxCYTcp-CO complex at 1.25 Å resolution shows that CO binds in two conformations moderated by the extent of displacement of the distal residue Leu16 toward the haem 7-propionate. The presence of two CO conformations is confirmed by cryogenic resonance Raman data. The preferred linear Fe-C-O arrangement (170 ± 8°) is accompanied by a flip of the propionate from the distal to proximal face of the haem. In the second conformation, the Fe-C-O unit is bent (158 ± 8°) with no flip of propionate. The energetic cost of the CO-induced Leu-propionate movements is reflected in a 600 mV (57.9 kJ mol(-1)) decrease in haem potential, a value in good agreement with density functional theory calculations. Substitution of Leu by Ala or Gly (structures determined at 1.03 and 1.04 Å resolutions) resulted in a haem site that binds CO in the linear mode only and where no significant change in redox potential is observed. Remarkably, these variants were isolated as ferrous 6c-CO complexes, attributable to the observed eight orders of magnitude increase in affinity for CO, including an approximately 10,000-fold decrease in the rate of dissociation. These new findings have wide implications for preventing CO poisoning of gas-binding haem proteins.

  • Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C'127Achromobacter xylosoxidansMutation(s): 1 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Explore P00138 
Go to UniProtKB:  P00138
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00138
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PCA
Experimental Data & Validation

Experimental Data

  • Resolution: 1.05 Å
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.506α = 90
b = 53.506β = 90
c = 181.574γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2014-08-20
    Changes: Data collection
  • Version 1.2: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 2.0: 2020-03-11
    Changes: Advisory, Derived calculations, Other, Polymer sequence
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description