3VEP

Crystal structure of SigD4 in complex with its negative regulator RsdA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of sigma-factor activity by proteolysis

Jaiswal, R.K.Prabha, T.S.Manjeera, G.Gopal, B.

(2013) Nucleic Acids Res. 41: 3414-3423

  • DOI: 10.1093/nar/gks1468
  • Primary Citation of Related Structures:  3VFZ

  • PubMed Abstract: 
  • The relative levels of different σ factors dictate the expression profile of a bacterium. Extracytoplasmic function σ factors synchronize the transcriptional profile with environmental conditions. The cellular concentration of free extracytoplasmic f ...

    The relative levels of different σ factors dictate the expression profile of a bacterium. Extracytoplasmic function σ factors synchronize the transcriptional profile with environmental conditions. The cellular concentration of free extracytoplasmic function σ factors is regulated by the localization of this protein in a σ/anti-σ complex. Anti-σ factors are multi-domain proteins with a receptor to sense environmental stimuli and a conserved anti-σ domain (ASD) that binds a σ factor. Here we describe the structure of Mycobacterium tuberculosis anti-σ(D) (RsdA) in complex with the -35 promoter binding domain of σ(D) (σ(D)4). We note distinct conformational features that enable the release of σ(D) by the selective proteolysis of the ASD in RsdA. The structural and biochemical features of the σ(D)/RsdA complex provide a basis to reconcile diverse regulatory mechanisms that govern σ/anti-σ interactions despite high overall structural similarity. Multiple regulatory mechanisms embedded in an ASD scaffold thus provide an elegant route to rapidly re-engineer the expression profile of a bacterium in response to an environmental stimulus.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein Rv3413c/MT3522
X, C, G, J
80Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rsdA
Find proteins for P9WJ71 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WJ71
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable RNA polymerase sigma-D factor
D, A, E, H
86Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: sigD
Find proteins for P9WGG9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGG9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, D, E, H, X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C, D, E, G, H, J, X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.740α = 90.00
b = 110.720β = 133.00
c = 73.130γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
MOSFLMdata reduction
SCALAdata scaling
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references