2LFW

NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria.

Campagne, S.Damberger, F.F.Kaczmarczyk, A.Francez-Charlot, A.Allain, F.H.Vorholt, J.A.

(2012) Proc Natl Acad Sci U S A 109: E1405-E1414

  • DOI: 10.1073/pnas.1117003109
  • Primary Citation of Related Structures:  
    2LFW

  • PubMed Abstract: 
  • Reprogramming gene expression is an essential component of adaptation to changing environmental conditions. In bacteria, a widespread mechanism involves alternative sigma factors that redirect transcription toward specific regulons. The activity of sigma factors is often regulated through sequestration by cognate anti-sigma factors; however, for most systems, it is not known how the activity of the anti-sigma factor is controlled to release the sigma factor ...

    Reprogramming gene expression is an essential component of adaptation to changing environmental conditions. In bacteria, a widespread mechanism involves alternative sigma factors that redirect transcription toward specific regulons. The activity of sigma factors is often regulated through sequestration by cognate anti-sigma factors; however, for most systems, it is not known how the activity of the anti-sigma factor is controlled to release the sigma factor. Recently, the general stress response sigma factor in Alphaproteobacteria, σ(EcfG), was identified. σ(EcfG) is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. This key regulator sequesters NepR upon phosphorylation of its PhyR receiver domain via its σ(EcfG) sigma factor-like output domain (PhyR(SL)). To understand the molecular basis of the PhyR-mediated partner-switching mechanism, we solved the structure of the PhyR(SL)-NepR complex using NMR. The complex reveals an unprecedented anti-sigma factor binding mode: upon PhyR(SL) binding, NepR forms two helices that extend over the surface of the PhyR(SL) subdomains. Homology modeling and comparative analysis of NepR, PhyR(SL), and σ(EcfG) mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. A lower density of hydrophobic interactions, together with the absence of specific polar contacts in the σ(EcfG)-NepR complex model, is consistent with the higher affinity of NepR for PhyR compared with σ(EcfG). Finally, by reconstituting the partner switch in vitro, we demonstrate that the difference in affinity of NepR for its partners is sufficient for the switch to occur.


    Organizational Affiliation

    Institute of Microbiology, Eidgenössiche Technische Hochschule Zurich, 8093 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PhyR sigma-like domainA157Sphingomonas sp. Fr1Mutation(s): 0 
Gene Names: phyR
Find proteins for G8HXE0 (Sphingomonas sp. Fr1)
Explore G8HXE0 
Go to UniProtKB:  G8HXE0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NepR anti sigma factorB62Sphingomonas sp. Fr1Mutation(s): 0 
Gene Names: nepR
Find proteins for G8HXD9 (Sphingomonas sp. Fr1)
Explore G8HXD9 
Go to UniProtKB:  G8HXD9
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 2LFW Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references
  • Version 1.2: 2012-06-06
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary