3GZ6 | pdb_00003gz6

Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.247 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3GZ6

This is version 1.6 of the entry. See complete history

Literature

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism

Huang, N.De Ingeniis, J.Galeazzi, L.Mancini, C.Korostelev, Y.D.Rakhmaninova, A.B.Gelfand, M.S.Rodionov, D.A.Raffaelli, N.Zhang, H.

(2009) Structure 17: 939-951

  • DOI: https://doi.org/10.1016/j.str.2009.05.012
  • Primary Citation Related Structures: 
    3GZ5, 3GZ6, 3GZ8

  • PubMed Abstract: 

    Besides its function as an essential redox cofactor, nicotinamide adenine dinucleotide (NAD) also serves as a consumable substrate for several reactions with broad impact on many cellular processes. NAD homeostasis appears to be tightly controlled, but the mechanism of its regulation is little understood. Here we demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses the transcription of NAD biosynthetic genes in vitro. The NAD metabolite ADP-ribose functions as an activator suppressing NrtR repressor activity. The presence of high ADP-ribose levels in the cell is indicative of active NAD turnover in bacteria, which could signal the activation of NAD biosynthetic gene expression via inhibiting the repressor function of NrtR. By comparing the crystal structures of NrtR in complex with DNA and with ADP-ribose, we identified a "Nudix switch" element that likely plays a critical role in the allosteric regulation of DNA binding and repressor function of NrtR.


  • Organizational Affiliation
    • Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecule Content 

  • Total Structure Weight: 71.15 kDa 
  • Atom Count: 4,729 
  • Modeled Residue Count: 492 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MutT/nudix family proteinA,
C [auth B]
240Shewanella oneidensisMutation(s): 0 
Gene Names: NrtRSO_1979
UniProt
Find proteins for Q8EFJ3 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EFJ3 
Go to UniProtKB:  Q8EFJ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EFJ3
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (27-MER)B [auth D]27N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (27-MER)D [auth C]27N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.247 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.58α = 90
b = 159.58β = 90
c = 73.067γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-01-11
    Changes: Other
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.6: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description