1E85

Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with NO bound to proximal side of heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 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, 1E86

  • 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: 
    • The Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and Their Implications for Four-Helix Bundles
      Dobbs, A.J.,Faber, H.R.,Anderson, B.F.,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
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 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: 1.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.035α = 90.00
b = 53.035β = 90.00
c = 180.993γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

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: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance