2YL7

CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G VARIANT AT 0.9 A RESOLUTION - RESTRAINT REFINEMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report



Literature

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: 10.1073/pnas.1109051108
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'A127Achromobacter xylosoxidansMutation(s): 1 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Explore P00138 
Go to UniProtKB:  P00138
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
CMO
Query on CMO

Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.377α = 90
b = 53.377β = 90
c = 181.652γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2012-06-13
    Changes: Other
  • Version 2.0: 2020-03-11
    Changes: Advisory, Atomic model, Derived calculations, Other, Polymer sequence