2J7A

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of the Membrane-Bound Cytochrome C Quinol Dehydrogenase Nrfh Reveals Novel Haem Coordination.

Rodrigues, M.L.Oliveira, T.F.Pereira, I.A.C.Archer, M.

(2006) Embo J. 25: 5951

  • DOI: 10.1038/sj.emboj.7601439

  • PubMed Abstract: 
  • Oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate ATP by oxidative phosphorylation. A novel family of cytochrome c quinol dehydrogenases that play an impor ...

    Oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate ATP by oxidative phosphorylation. A novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. Here, we describe the first structure of a cytochrome from this family, NrfH from Desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome c nitrite reductase NrfA. One NrfH molecule interacts with one NrfA dimer in an asymmetrical manner, forming a large membrane-bound complex with an overall alpha(4)beta(2) quaternary arrangement. The menaquinol-interacting NrfH haem is pentacoordinated, bound by a methionine from the CXXCHXM sequence, with an aspartate residue occupying the distal position. The NrfH haem that transfers electrons to NrfA has a lysine residue from the closest NrfA molecule as distal ligand. A likely menaquinol binding site, containing several conserved and essential residues, is identified.


    Related Citations: 
    • Crystallization and Preliminary Structure Determination of the Membrane-Bound Complex Cytochrome C Nitrite Reductase from Desulfovibrio Vulgaris Hildenborough
      Rodrigues, M.L.,Oliveira, T.,Matias, P.M.,Martins, I.C.,Valente, F.M.A.,Pereira, I.A.C.,Archer, M.
      (2006) Acta Crystallogr.,Sect.F 62: 565


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C NITRITE REDUCTASE NRFA
A, B, D, E, G, H, J, K, M, N, P, Q
500Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: nrfA
EC: 1.7.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
NrfH Cytochrome C Quinol Dehydrogenase
Find proteins for Q72EF3 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72EF3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C QUINOL DEHYDROGENASE NRFH
C, F, I, L, O, R
159Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
NrfH Cytochrome C Quinol Dehydrogenase
Find proteins for Q72EF4 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72EF4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
C, I, O
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, D, E, G, H, J, K, M, N, P, Q
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
C, F, I, L, O, R
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.664α = 90.00
b = 258.117β = 90.00
c = 580.742γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHARPphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance