3IR6

Crystal structure of NarGHI mutant NarG-H49S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.

Rothery, R.A.Bertero, M.G.Spreter, T.Bouromand, N.Strynadka, N.C.Weiner, J.H.

(2010) J.Biol.Chem. 285: 8801-8807

  • DOI: 10.1074/jbc.M109.066027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli ...

    We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). Cys and Ser mutants of NarG-His(49) both lack catalytic activity, with only the former assembling FS0 and Mo-bisPGD. Importantly, both prosthetic groups are absent in the NarG-H49S mutant. EPR spectroscopy of the Cys mutant reveals that the E(m) value of the FS0 cluster is decreased by at least 500 mV, preventing its participation in electron transfer to the Mo-bisPGD cofactor. To demonstrate that decreasing the FS0 cluster E(m) results in decreased enzyme activity, we mutated a critical Arg residue (NarG-Arg(94)) in the vicinity of FS0 to a Ser residue. In this case, the E(m) of FS0 is decreased by 115 mV, with a concomitant decrease in enzyme turnover to approximately 30% of the wild type. Analysis of the structure of the NarG-H49S mutant reveals two important aspects of NarGHI maturation: (i) apomolybdo-NarGHI is able to bind GDP moieties at their respective P and Q sites in the absence of the Mo-bisPGD cofactor, and (ii) a critical segment of residues in NarG, (49)HGVNCTG(55), must be correctly positioned to ensure holoenzyme maturation.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 alpha chain
A
1247Escherichia coli (strain K12)Mutation(s): 1 
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
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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Respiratory nitrate reductase 1 gamma chain
C
225Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: narI (chlI)
EC: 1.7.5.1
Find proteins for P11350 (Escherichia coli (strain K12))
Go to UniProtKB:  P11350
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
AGA
Query on AGA

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Download CCD File 
A
(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
PHOSPHATIDYL GLYCEROL
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
 Ligand Interaction
F3S
Query on F3S

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

Download SDF File 
Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 154.142α = 90.00
b = 239.825β = 90.00
c = 139.873γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description