2J7A

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 2.1 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
  • Primary Citation of Related Structures:  
    2J7A

  • 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 important role in bacterial respiratory chains was recognised in recent years ...

    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 Struct Biol Cryst Commun 62: 565
    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C NITRITE REDUCTASE NRFAA, B, D, E, G, H, J, K, A,  B,  D,  E,  G,  H,  J,  K,  M,  N,  P,  Q
500Desulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: nrfA, DVU_0625
EC: 1.7.2.2
Membrane protein
Mpstruc		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))
Explore Q72EF3 
Go to UniProtKB:  Q72EF3
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C QUINOL DEHYDROGENASE NRFH C, F, I, L, O, R159Desulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: DVU_0624
Membrane protein
Mpstruc		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))
Explore Q72EF4 
Go to UniProtKB:  Q72EF4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
LMT
Query on LMT
Download Ideal Coordinates CCD File 
C, F, I, L, O, R
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C, I, O
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B, D, E, G, H, J, K, M, N, P, Q
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.664α = 90
b = 258.117β = 90
c = 580.742γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-06
    Type: Initial release
  • Version 2.0: 2019-09-25
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
  • Version 2.1: 2019-11-06
    Changes: Data collection, Refinement description