6MAB | pdb_00006mab

1.7A resolution structure of RsbU from Chlamydia trachomatis (periplasmic domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.197 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6MAB

This is version 1.5 of the entry. See complete history

Literature

Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation.

Soules, K.R.Dmitriev, A.LaBrie, S.D.Dimond, Z.E.May, B.H.Johnson, D.K.Zhang, Y.Battaile, K.P.Lovell, S.Hefty, P.S.

(2020) Mol Microbiol 113: 68-88

  • DOI: https://doi.org/10.1111/mmi.14401
  • Primary Citation Related Structures: 
    6MAB

  • PubMed Abstract: 

    Chlamydia trachomatis is an obligate intracellular bacteria that undergo dynamic morphologic and physiologic conversions upon gaining an access to a eukaryotic cell. These conversions likely require the detection of key environmental conditions and regulation of metabolic activity. Chlamydia encodes homologs to proteins in the Rsb phosphoregulatory partner-switching pathway, best described in Bacillus subtilis. ORF CT588 has a strong sequence similarity to RsbU cytoplasmic phosphatase domain but also contains a unique periplasmic sensor domain that is expected to control the phosphatase activity. A 1.7 Å crystal structure of the periplasmic domain of the RsbU protein from C. trachomatis (PDB 6MAB) displays close structural similarity to DctB from Vibrio and Sinorhizobium. DctB has been shown, both structurally and functionally, to specifically bind to the tricarboxylic acid (TCA) cycle intermediate succinate. Surface plasmon resonance and differential scanning fluorimetry of TCA intermediates and potential metabolites from a virtual screen of RsbU revealed that alpha-ketoglutarate, malate and oxaloacetate bound to the RsbU periplasmic domain. Substitutions in the putative binding site resulted in reduced binding capabilities. An RsbU null mutant showed severe growth defects which could be restored through genetic complementation. Chemical inhibition of ATP synthesis by oxidative phosphorylation phenocopied the growth defect observed in the RsbU null strain. Altogether, these data support a model with the Rsb system responding differentially to TCA cycle intermediates to regulate metabolism and key differentiation processes.


  • Organizational Affiliation
    • Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.

Macromolecule Content 

  • Total Structure Weight: 30.79 kDa 
  • Atom Count: 2,304 
  • Modeled Residue Count: 269 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sigma regulatory family protein-PP2C phosphatase272Chlamydia trachomatis L2/434/BuMutation(s): 0 
Gene Names: rbsUCTL0851
UniProt
Find proteins for A0A0H3MDU0 (Chlamydia trachomatis serovar L2 (strain ATCC VR-902B / DSM 19102 / 434/Bu))
Explore A0A0H3MDU0 
Go to UniProtKB:  A0A0H3MDU0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3MDU0
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on IPA



Download:Ideal Coordinates CCD File
B [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.197 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.712α = 90
b = 96.712β = 90
c = 65.385γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesP30 GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2020-02-19
    Changes: Database references
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references