1W2G

Crystal Structure Of Mycobacterium Tuberculosis Thymidylate Kinase Complexed With Deoxythymidine (dT) (2.1 A Resolution)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of Mycobacterium Tuberculosis Thymidylate Kinase in Complex with 3'-Azidodeoxythymidine Monophosphate Suggests a Mechanism for Competitive Inhibition

Fioravanti, E.Adam, V.Munier-Lehmann, H.Bourgeois, D.

(2005) Biochemistry 44: 130

  • DOI: 10.1021/bi0484163
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis thymidylate kinase (TMPK(Mtub)) catalyzes the ATP-dependent phosphorylation of deoxythymidine 5'-monophosphate (dTMP). Essential to DNA replicat ...

    Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis thymidylate kinase (TMPK(Mtub)) catalyzes the ATP-dependent phosphorylation of deoxythymidine 5'-monophosphate (dTMP). Essential to DNA replication, this enzyme represents a promising target for developing new drugs against TB, because the configuration of its active site is unique within the TMPK family. Indeed, it has been proposed that, as opposed to other TMPKs, catalysis by TMPK(Mtub) necessitates the transient binding of a magnesium ion coordinating the phosphate acceptor. Moreover, 3'-azidodeoxythymidine monophosphate (AZTMP) is a competitive inhibitor of TMPK(Mtub), whereas it is a substrate for human and other TMPKs. Here, the crystal structures of TMPK(Mtub) in complex with deoxythymidine (dT) and AZTMP were determined to 2.1 and 2.0 A resolution, respectively, and suggest a mechanism for inhibition. The azido group of AZTMP perturbs the induced-fit mechanism normally adopted by the enzyme. Magnesium is prevented from binding, and the resulting electrostatic environment precludes phosphoryl transfer from occurring. Our data provide a model for drug development against tuberculosis.


    Organizational Affiliation

    LCCP, UMR 5075, IBS-CEA/CNRS/UJF, 41 avenue Jules Horowitz, 38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE TMK
A, B
214Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: tmk
EC: 2.7.4.9
Find proteins for P9WKE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
THM
Query on THM

Download SDF File 
Download CCD File 
A, B
THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THMKi: 27000 - 715000 nM (100) BINDINGDB
THMKi: 27000 nM BINDINGMOAD
THMKi: 27000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.865α = 90.00
b = 63.865β = 90.00
c = 195.336γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-12
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-05-02
    Type: Data collection