1OGY

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase

Arnoux, P.Sabaty, M.Alric, J.Frangioni, B.Guigliarelli, B.Adriano, J.-M.Pignol, D.

(2003) Nat.Struct.Mol.Biol. 10: 928

  • DOI: 10.1038/nsb994

  • PubMed Abstract: 
  • The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme ele ...

    The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme electron transfer small subunit NapB binds to the large subunit with heme II in close proximity to the [4Fe-4S] cluster of NapA. A total of 57 residues at the N- and C-terminal extremities of NapB adopt an extended conformation, embracing the NapA subunit and largely contributing to the total area of 5,900 A(2) buried in the complex. Complex formation was studied further by measuring the variation of the redox potentials of all the cofactors upon binding. The marked effects observed are interpreted in light of the three-dimensional structure and depict a plasticity that contributes to an efficient electron transfer in the complex from the heme I of NapB to the molybdenum catalytic site of NapA.


    Related Citations: 
    • The 1.25 A Resolution Structure of the Diheme Napb Subunit of Soluble Nitrate Reductase Reveals a Novel Cytochrome C Fold with a Stacked Heme Arrangement
      Brige, A.,Leys, D.,Meyer, T.E.,Cusanovich, M.A.,Van Beeumen, J.J.
      (2002) Biochemistry 41: 4827
    • Crystal Structure of the First Dissimilatory Nitrate Reductase (Nap) at 1.9 A Solved by MAD Methods
      Dias, J.M.,Than, M.,Humm, A.,Huber, R.,Bourenkov, G.,Bartunik, H.,Bursakov, S.,Calvete, J.,Caldeira, J.,Carneiro, C.,Moura, J.,Moura, I.,Romao, M.J.
      (1999) Structure 7: 65


    Organizational Affiliation

    CEA/Cadarache, DSV, DEVM, Laboratoire de Bioénergétique Cellulaire, 13108 St Paul lez Durance Cedex, France. pascal.arnoux@cea.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC NITRATE REDUCTASE
A, C, E, G, I, K, M, O
802Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Mutation(s): 0 
Gene Names: napA
EC: 1.9.6.1
Find proteins for Q53176 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q53176
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
B, D, F, H, J, L, N, P
130Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)Mutation(s): 0 
Gene Names: napB
Find proteins for Q53177 (Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158))
Go to UniProtKB:  Q53177
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MO
Query on MO

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B, D, F, H, J, L, N, P
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
MGD
Query on MGD

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 123.000α = 90.00
b = 225.200β = 92.10
c = 154.600γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance