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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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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 alpha chainA1247Escherichia 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 beta chainB512Escherichia 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))
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Go to UniProtKB:  P11349
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 gamma chainC225Escherichia 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MD1 (Subject of Investigation/LOI)
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		 Ligand Interaction
3PH (Subject of Investigation/LOI)
Query on 3PH
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 M [auth B]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N		 Ligand Interaction
HEM (Subject of Investigation/LOI)
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		 Ligand Interaction
AGA (Subject of Investigation/LOI)
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		 Ligand Interaction
SF4
Query on SF4
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 G [auth A], I [auth B], J [auth B], K [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
 L [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
6MO
Query on 6MO
Download Ideal Coordinates CCD File 
 F [auth A]MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME		CL-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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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