1Y4Z

The crystal structure of Nitrate Reductase A, NarGHI, in complex with the Q-site inhibitor pentachlorophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A

Bertero, M.G.Rothery, R.A.Boroumand, N.Palak, M.Blasco, F.Ginet, N.Weiner, J.H.Strynadka, N.C.J.

(2005) J Biol Chem 280: 14836-14843

  • DOI: 10.1074/jbc.M410457200
  • Primary Citation of Related Structures:  
    1Y5L, 1Y5I, 1Y4Z, 1Y5N

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in complex with pentachlorophenol has been determined to 2.0 A of resolution. We have shown that pentachlorophenol is a potent inhibitor of quinol:nitrate oxidoreductase activity and that it also perturbs the EPR spectrum of one of the hemes located in the membrane anchoring subunit (NarI) ...

    The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in complex with pentachlorophenol has been determined to 2.0 A of resolution. We have shown that pentachlorophenol is a potent inhibitor of quinol:nitrate oxidoreductase activity and that it also perturbs the EPR spectrum of one of the hemes located in the membrane anchoring subunit (NarI). This new structural information together with site-directed mutagenesis data, biochemical analyses, and molecular modeling provide the first molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI. A possible proton conduction pathway linked to electron transfer reactions has also been defined, providing fundamental atomic details of ubiquinol oxidation by NarGHI at the bacterial membrane.


    Organizational Affiliation

    Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 alpha chainA1246Escherichia 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 beta chainB512Escherichia coliMutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
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
HEM
Query on HEM

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M [auth C], N [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
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
 Ligand Interaction
SF4
Query on SF4

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G [auth A], I [auth B], K [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
J [auth B], L [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
PCI
Query on PCI

Download Ideal Coordinates CCD File 
O [auth C]PENTACHLOROPHENOL
C6 H Cl5 O
IZUPBVBPLAPZRR-UHFFFAOYSA-N
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PCIKi :  57   nM  PDBBind
PCIKi:  57   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.456α = 90
b = 241.342β = 90
c = 140.014γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance