6OD1

IraD-bound to RssB D58P variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for inhibition of a response regulator of sigmaSstability by a ClpXP antiadaptor.

Dorich, V.Brugger, C.Tripathi, A.Hoskins, J.R.Tong, S.Suhanovsky, M.M.Sastry, A.Wickner, S.Gottesman, S.Deaconescu, A.M.

(2019) Genes Dev 33: 718-732

  • DOI: 10.1101/gad.320168.118
  • Primary Citation of Related Structures:  
    6OD1

  • PubMed Abstract: 
  • The stationary phase promoter specificity subunit σ S (RpoS) is delivered to the ClpXP machinery for degradation dependent on the adaptor RssB. This adaptor-specific degradation of σ S provides a major point for regulation and transcriptional reprogramming during the general stress response ...

    The stationary phase promoter specificity subunit σ S (RpoS) is delivered to the ClpXP machinery for degradation dependent on the adaptor RssB. This adaptor-specific degradation of σ S provides a major point for regulation and transcriptional reprogramming during the general stress response. RssB is an atypical response regulator and the only known ClpXP adaptor that is inhibited by multiple but dissimilar antiadaptors (IraD, IraP, and IraM). These are induced by distinct stress signals and bind to RssB in poorly understood manners to achieve stress-specific inhibition of σ S turnover. Here we present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structure reveals that RssB adopts a compact closed architecture with extensive interactions between its N-terminal and C-terminal domains. The structural data, together with mechanistic studies, suggest that RssB plasticity, conferred by an interdomain glutamate-rich flexible linker, is critical for regulation of σ S degradation. Structural modulation of interdomain linkers may thus constitute a general strategy for tuning response regulators.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Regulator of RpoSA337Escherichia coli 907672Mutation(s): 1 
Gene Names: rssBHMPREF1595_01509
UniProt
Find proteins for V0SNG0 (Escherichia coli 907672)
Explore V0SNG0 
Go to UniProtKB:  V0SNG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV0SNG0
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-adapter protein IraDB115Escherichia coli K-12Mutation(s): 0 
Gene Names: iraDyjiDb4326JW5782
UniProt
Find proteins for P39375 (Escherichia coli (strain K12))
Explore P39375 
Go to UniProtKB:  P39375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39375
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.938α = 90
b = 55.938β = 90
c = 300.298γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM121975

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence