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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 beta chain
B
512Escherichia coliMutation(s): 1 
Gene Names: narH
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
NarGHI Nitrate Reductase with pentachlorophenol (PCP)
Find proteins for P11349 (Escherichia coli (strain K12))
Go to UniProtKB:  P11349

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 gamma chain
C
225Escherichia coliMutation(s): 1 
Gene Names: narI
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
NarGHI Nitrate Reductase with pentachlorophenol (PCP)
Find proteins for P11350 (Escherichia coli (strain K12))
Go to UniProtKB:  P11350

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 alpha chain
A
1246Escherichia coliMutation(s): 0 
Gene Names: narG
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
NarGHI Nitrate Reductase with pentachlorophenol (PCP)
Find proteins for P09152 (Escherichia coli (strain K12))
Go to UniProtKB:  P09152
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MD1
Query on MD1

Download CCD File 
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

Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
AGA
Query on AGA

Download CCD File 
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

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

Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
PCI
Query on PCI

Download CCD File 
C
PENTACHLOROPHENOL
C6 H Cl5 O
IZUPBVBPLAPZRR-UHFFFAOYSA-N
 Ligand Interaction
6MO
Query on 6MO

Download CCD File 
A
MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C
L-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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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