4ZIL

Crystal structure of Rv2466c and oxidoreductase from Mycobacterium tuberculosis in its reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.507 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053.

Albesa-Jove, D.Comino, N.Tersa, M.Mohorko, E.Urresti, S.Dainese, E.Chiarelli, L.R.Pasca, M.R.Manganelli, R.Makarov, V.Riccardi, G.Svergun, D.I.Glockshuber, R.Guerin, M.E.

(2015) J.Biol.Chem. 290: 31077-31089

  • DOI: 10.1074/jbc.M115.677039

  • PubMed Abstract: 
  • Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer i ...

    Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer in which each subunit displays a modular architecture comprising a canonical thioredoxin-fold with a Cys(19)-Pro(20)-Trp(21)-Cys(22) motif, and an insertion consisting of a four α-helical bundle and a short α-helical hairpin. Strong evidence is provided for dramatic conformational changes during the Rv2466c redox cycle, which are essential for TP053 activity. Strikingly, a new crystal structure of the reduced form of Rv2466c revealed the binding of a C-terminal extension in α-helical conformation to a pocket next to the active site cysteine pair at the interface between the thioredoxin domain and the helical insertion domain. The ab initio low-resolution envelopes obtained from small angle x-ray scattering showed that the fully reduced form of Rv2466c adopts a "closed" compact conformation in solution, similar to that observed in the crystal structure. In contrast, the oxidized form of Rv2466c displays an "open" conformation, where tertiary structural changes in the α-helical subdomain suffice to account for the observed conformational transitions. Altogether our structural, biochemical, and biophysical data strongly support a model in which the formation of the catalytic disulfide bond upon TP053 reduction triggers local structural changes that open the substrate binding site of Rv2466c allowing the release of the activated, reduced form of TP053. Our studies suggest that similar structural changes might have a functional role in other members of the thioredoxin-fold superfamily.


    Organizational Affiliation

    the Departments of Molecular Medicine and.,the A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia, and.,the European Molecular Biology Laboratory, Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, D-22603 Hamburg, Germany.,the Institute for Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain, mrcguerin@gmail.com.,Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy.,From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain.,From the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain, the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain, the IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DSBA oxidoreductase
A, B
220Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Find proteins for O53193 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O53193
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.507 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.649α = 90.00
b = 46.814β = 97.97
c = 104.308γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2016-01-27
    Type: Structure summary