1Q16

Crystal structure of Nitrate Reductase A, NarGHI, from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A

Bertero, M.G.Rothery, R.A.Palak, M.Hou, C.Lim, D.Blasco, F.Weiner, J.H.Strynadka, N.C.J.

(2003) Nat Struct Biol 10: 681-687

  • DOI: https://doi.org/10.1038/nsb969
  • Primary Citation of Related Structures:  
    1Q16

  • PubMed Abstract: 

    The facultative anaerobe Escherichia coli is able to assemble specific respiratory chains by synthesis of appropriate dehydrogenases and reductases in response to the availability of specific substrates. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (nitrate reductase A; NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. We present here the crystal structure of NarGHI at a resolution of 1.9 A. The NarGHI structure identifies the number, coordination scheme and environment of the redox-active prosthetic groups, a unique coordination of the molybdenum atom, the first structural evidence for the role of an open bicyclic form of the molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) cofactor in the catalytic mechanism and a novel fold of the membrane anchor subunit. Our findings provide fundamental molecular details for understanding the mechanism of proton-motive force generation by a redox loop.


  • Organizational Affiliation

    Department of Biochemistry, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 alpha chain1,247Escherichia coliMutation(s): 0 
Gene Names: narG
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P09152 (Escherichia coli (strain K12))
Explore P09152 
Go to UniProtKB:  P09152
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09152
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 beta chain512Escherichia coliMutation(s): 0 
Gene Names: narH
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P11349 (Escherichia coli (strain K12))
Explore P11349 
Go to UniProtKB:  P11349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11349
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 gamma chain225Escherichia coliMutation(s): 1 
Gene Names: narI
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P11350 (Escherichia coli (strain K12))
Explore P11350 
Go to UniProtKB:  P11350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11350
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MD1
Query on MD1

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
C20 H26 N10 O13 P2 S2
IRGDLSAXQOKWLX-XHEYTWMPSA-N
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
M [auth B]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
HEM
Query on HEM

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N [auth C],
O [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
AGA
Query on AGA

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H [auth A](1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
J [auth B],
K [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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L [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
6MO
Query on 6MO

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F [auth A]MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
C
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.175α = 90
b = 241.376β = 90
c = 139.494γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
SHARPphasing
RESOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary