3ML1

Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states

Coelho, C.Gonzalez, P.J.Moura, J.J.G.Moura, I.Trincao, J.Romao, M.J.

(2011) J.Mol.Biol. 408: 932-948

  • DOI: 10.1016/j.jmb.2011.03.016
  • Primary Citation of Related Structures:  3O5A

  • PubMed Abstract: 
  • The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein ...

    The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit (NapA, 91 kDa) containing the molybdenum active site plus one [4Fe-4S] cluster, as well as a small subunit (NapB, 17 kDa), which is a diheme c-type cytochrome involved in electron transfer. Crystals of the oxidized form of the enzyme diffracted beyond 1.5 Å at the European Synchrotron Radiation Facility. This is the highest resolution reported to date for a nitrate reductase, providing true atomic details of the protein active center, and this showed further evidence on the molybdenum coordination sphere, corroborating previous data on the related Desulfovibrio desulfuricans NapA. The molybdenum atom is bound to a total of six sulfur atoms, with no oxygen ligands or water molecules in the vicinity. In the present work, we were also able to prepare partially reduced crystals that revealed two alternate conformations of the Mo-coordinating cysteine. This crystal form was obtained by soaking dithionite into crystals grown in the presence of the ionic liquid [C(4)mim]Cl(-). In addition, UV-Vis and EPR spectroscopy studies showed that the periplasmic nitrate reductase from C. necator might work at unexpectedly high redox potentials when compared to all periplasmic nitrate reductases studied to date.


    Organizational Affiliation

    REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic nitrate reductase
A
802Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)Gene Names: napA
EC: 1.7.99.4
Find proteins for P39185 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Go to UniProtKB:  P39185
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Diheme cytochrome c napB
B
135Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)Gene Names: napB
Find proteins for P39186 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Go to UniProtKB:  P39186
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
MOS
Query on MOS

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Download CCD File 
A
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
MGD
Query on MGD

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Download CCD File 
A
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: 1.6 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.202α = 90.00
b = 82.384β = 100.72
c = 96.837γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
DMphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-12-07
    Type: Database references