4ILQ

2.60A resolution structure of CT771 from Chlamydia trachomatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Chlamydia trachomatis CT771 (nudH) Is an Asymmetric Ap4A Hydrolase.

Barta, M.L.Lovell, S.Sinclair, A.N.Battaile, K.P.Hefty, P.S.

(2014) Biochemistry 53: 214-224

  • DOI: 10.1021/bi401473e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Asymmetric diadenosine 5',5‴-P(1),P(4)-tetraphosphate (Ap4A) hydrolases are members of the Nudix superfamily that asymmetrically cleave the metabolite Ap4A into ATP and AMP while facilitating homeostasis. The obligate intracellular mammalian pathogen ...

    Asymmetric diadenosine 5',5‴-P(1),P(4)-tetraphosphate (Ap4A) hydrolases are members of the Nudix superfamily that asymmetrically cleave the metabolite Ap4A into ATP and AMP while facilitating homeostasis. The obligate intracellular mammalian pathogen Chlamydia trachomatis possesses a single Nudix family protein, CT771. As pathogens that rely on a host for replication and dissemination typically have one or zero Nudix family proteins, this suggests that CT771 could be critical for chlamydial biology and pathogenesis. We identified orthologues to CT771 within environmental Chlamydiales that share active site residues suggesting a common function. Crystal structures of both apo- and ligand-bound CT771 were determined to 2.6 Å and 1.9 Å resolution, respectively. The structure of CT771 shows a αβα-sandwich motif with many conserved elements lining the putative Nudix active site. Numerous aspects of the ligand-bound CT771 structure mirror those observed in the ligand-bound structure of the Ap4A hydrolase from Caenorhabditis elegans. These structures represent only the second Ap4A hydrolase enzyme member determined from eubacteria and suggest that mammalian and bacterial Ap4A hydrolases might be more similar than previously thought. The aforementioned structural similarities, in tandem with molecular docking, guided the enzymatic characterization of CT771. Together, these studies provide the molecular details for substrate binding and specificity, supporting the analysis that CT771 is an Ap4A hydrolase (nudH).


    Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CT771
A
153Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B)Mutation(s): 0 
Find proteins for A0A0H3MCJ9 (Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B))
Go to UniProtKB:  A0A0H3MCJ9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.351α = 90.00
b = 116.351β = 90.00
c = 84.112γ = 120.00
Software Package:
Software NamePurpose
JDirectordata collection
BALBESphasing
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references, Other
  • Version 1.2: 2014-01-29
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description