1E86

Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with CO bound to distal side of heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unprecedented Proximal Binding of Nitric Oxide to Heme: Implications for Guanylate Cyclase

Lawson, D.M.Stevenson, C.E.M.Andrew, C.R.Eady, R.R.

(2000) Embo J. 19: 5661

  • DOI: 10.1093/emboj/19.21.5661
  • Primary Citation of Related Structures:  1E83, 1E84, 1E85

  • PubMed Abstract: 
  • Microbial cytochromes c' contain a 5-coordinate His-ligated heme that forms stable adducts with nitric oxide (NO) and carbon monoxide (CO), but not with dioxygen. We report the 1.95 and 1.35 A resolution crystal structures of the CO- and NO-bound for ...

    Microbial cytochromes c' contain a 5-coordinate His-ligated heme that forms stable adducts with nitric oxide (NO) and carbon monoxide (CO), but not with dioxygen. We report the 1.95 and 1.35 A resolution crystal structures of the CO- and NO-bound forms of the reduced protein from Alcaligenes xylosoxidans. NO disrupts the His-Fe bond and binds in a novel mode to the proximal face of the heme, giving a 5-coordinate species. In contrast, CO binds 6-coordinate on the distal side. A second CO molecule, not bound to the heme, is located in the proximal pocket. Since the unusual spectroscopic properties of cytochromes c' are shared by soluble guanylate cyclase (sGC), our findings have potential implications for the activation of sGC induced by the binding of NO or CO to the heme domain.


    Related Citations: 
    • Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures.
      Dobbs, A.J.,Anderson, B.F.,Faber, H.R.,Baker, E.N.
      (1996) Acta Crystallogr.,Sect.D 52: 356


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. david.lawson@bbsrc.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A
127Alcaligenes xylosoxydans xylosoxydansN/A
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P00138
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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

Download SDF File 
Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.639α = 90.00
b = 53.639β = 90.00
c = 180.935γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-06
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance