4W97

Structure of ketosteroid transcriptional regulator KstR2 of Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of a Ketosteroid Transcriptional Regulator of Mycobacterium tuberculosis.

Crowe, A.M.Stogios, P.J.Casabon, I.Evdokimova, E.Savchenko, A.Eltis, L.D.

(2015) J.Biol.Chem. 290: 872-882

  • DOI: 10.1074/jbc.M114.607481

  • PubMed Abstract: 
  • Catabolism of host cholesterol is critical to the virulence of Mycobacterium tuberculosis and is a potential target for novel therapeutics. KstR2, a TetR family repressor (TFR), regulates the expression of 15 genes encoding enzymes that catabolize th ...

    Catabolism of host cholesterol is critical to the virulence of Mycobacterium tuberculosis and is a potential target for novel therapeutics. KstR2, a TetR family repressor (TFR), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (HIP). Binding of KstR2 to its operator sequences is relieved upon binding of HIP-CoA. A 1.6-Å resolution crystal structure of the KstR2(Mtb)·HIP-CoA complex reveals that the KstR2(Mtb) dimer accommodates two molecules of HIP-CoA. Each ligand binds in an elongated cleft spanning the dimerization interface such that the HIP and CoA moieties interact with different KstR2(Mtb) protomers. In isothermal titration calorimetry studies, the dimer bound 2 eq of HIP-CoA with high affinity (K(d) = 80 ± 10 nm) but bound neither HIP nor CoASH. Substitution of Arg-162 or Trp-166, residues that interact, respectively, with the diphosphate and HIP moieties of HIP-CoA, dramatically decreased the affinity of KstR2(Mtb) for HIP-CoA but not for its operator sequence. The variant of R162M that decreased the affinity for HIP-CoA (ΔΔG = 13 kJ mol(-1)) is consistent with the loss of three hydrogen bonds as indicated in the structural data. A 24-bp operator sequence bound two dimers of KstR2. Structural comparisons with a ligand-free rhodococcal homologue and a DNA-bound homologue suggest that HIP-CoA induces conformational changes of the DNA-binding domains of the dimer that preclude their proper positioning in the major groove of DNA. The results provide insight into KstR2-mediated regulation of expression of steroid catabolic genes and the determinants of ligand binding in TFRs.


    Organizational Affiliation

    the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439.,Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada.,the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439 alexei.savchenko@utoronto.ca.,From the Departments of Biochemistry and Molecular Biology and.,the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and.,From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada, leltis@mail.ubc.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional repressor KstR2
A
200Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: kstR2
Find proteins for P9WMB9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMB9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UCA
Query on UCA

Download SDF File 
Download CCD File 
A
S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-[(3aS,4S,7aS)-7a-methyl-1,5-bis(oxidanylidene)-2,3,3a,4,6,7-hexahydroinden-4-yl]propanethioate
HIP-CoA
C34 H52 N7 O19 P3 S
IWNWMTZIJPUDPV-MDQHZGBLSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UCAKd: 80 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 72.485α = 90.00
b = 90.476β = 129.68
c = 49.798γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-3000data reduction
PHENIXmodel building
MrBUMPphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-03
    Type: Database references
  • Version 1.2: 2015-01-21
    Type: Database references