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

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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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 of Related Structures:  

  • 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

    IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, IL, 60439, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sigma regulatory family protein-PP2C phosphatase272Chlamydia trachomatis 434/BuMutation(s): 0 
Gene Names: rbsUCTL0851
Find proteins for A0A0H3MDU0 (Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B))
Explore A0A0H3MDU0 
Go to UniProtKB:  A0A0H3MDU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3MDU0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IPA

Download Ideal Coordinates CCD File 
C3 H8 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • 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
PDB_EXTRACTdata extraction

Structure Validation

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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