4OMY

Crystal Structure of SeMet NolR from Sinorhizobium fredii in complex with oligo AT DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.062 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.

Lee, S.G.Krishnan, H.B.Jez, J.M.

(2014) Proc.Natl.Acad.Sci.USA 111: 6509-6514

  • DOI: 10.1073/pnas.1402243111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a rang ...

    The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.


    Organizational Affiliation

    Department of Biology, Washington University, St. Louis, MO 63130.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NolR
A, B, C, D
118Rhizobium frediiMutation(s): 0 
Gene Names: nolR
Find proteins for Q83TD2 (Rhizobium fredii)
Go to UniProtKB:  Q83TD2
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*AP*GP*TP*TP*AP*A)-3 )E,G22N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*TP*CP*AP*AP*TP*TP*A)-3 )F,H22N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.062 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.132 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 131.019α = 90.00
b = 131.019β = 90.00
c = 67.688γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000data collection
SHELXSphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-06-04
    Type: Database references