1R27

Crystal Structure of NarGH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes

Jormakka, M.Richardson, D.Byrne, B.Iwata, S.

(2004) Structure 12: 95-104


  • PubMed Abstract: 
  • The structure of the catalytic and electron-transfer subunits (NarGH) of the integral membrane protein, respiratory nitrate reductase (Nar) has been determined to 2.0 A resolution revealing the molecular architecture of this Mo-bisMGD (molybdopterin- ...

    The structure of the catalytic and electron-transfer subunits (NarGH) of the integral membrane protein, respiratory nitrate reductase (Nar) has been determined to 2.0 A resolution revealing the molecular architecture of this Mo-bisMGD (molybdopterin-guanine-dinucleotide) containing enzyme which includes a previously undetected FeS cluster. Nar, together with the related enzyme formate dehydrogenase (Fdh-N), is a key enzyme in the generation of proton motive force across the membrane in Escherichia coli nitrate respiration. A comparative study revealed that Nar and Fdh-N employ different approaches for acquiring substrate, reflecting different catalytic mechanisms. Nar uses a very narrow and nonpolar substrate-conducting cavity with a nonspecific substrate binding site, whereas Fdh-N accommodates a wider, positively charged substrate-conducting cavity with a more specific substrate binding site. The Nar structure also demonstrates the first example of an Asp side chain acting as a Mo ligand providing a structural basis for the classification of Mo-bisMGD enzymes.


    Organizational Affiliation

    Division of Biomedical Sciences, Imperial College London, SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 alpha chain
A, C
1246Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: narG (bisD, narC)
EC: 1.7.5.1
Find proteins for P09152 (Escherichia coli (strain K12))
Go to UniProtKB:  P09152
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 beta chain
B, D
512Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: narH
EC: 1.7.5.1
Find proteins for P11349 (Escherichia coli (strain K12))
Go to UniProtKB:  P11349
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B, D
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MO
Query on MO

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Download CCD File 
A, C
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

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Download CCD File 
A, C
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: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.401α = 90.00
b = 298.300β = 90.00
c = 296.853γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
DMphasing
SCALEPACKdata scaling
CNSrefinement
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance