1G3U

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution.

Li de la Sierra, I.Munier-Lehmann, H.Gilles, A.M.Barzu, O.Delarue, M.

(2001) J.Mol.Biol. 311: 87-100

  • DOI: 10.1006/jmbi.2001.4843
  • Also Cited By: 1GTV, 1GSI

  • PubMed Abstract: 
  • The X-ray structure of Mycobacterium tuberculosis TMP kinase at 1.95 A resolution is described as a binary complex with its natural substrate TMP. Its main features involve: (i) a clear magnesium-binding site; (ii) an alpha-helical conformation for t ...

    The X-ray structure of Mycobacterium tuberculosis TMP kinase at 1.95 A resolution is described as a binary complex with its natural substrate TMP. Its main features involve: (i) a clear magnesium-binding site; (ii) an alpha-helical conformation for the so-called LID region; and (iii) a high density of positive charges in the active site. There is a network of interactions involving highly conserved side-chains of the protein, the magnesium ion, a sulphate ion mimicking the beta phosphate group of ATP and the TMP molecule itself. All these interactions conspire in stabilizing what appears to be the closed form of the enzyme. A complete multialignment of all (32) known sequences of TMP kinases is presented. Subtle differences in the TMP binding site were noted, as compared to the Escherichia coli, yeast and human enzyme structures, which have been reported recently. These differences could be used to design specific inhibitors of this essential enzyme of nucleotide metabolism. Two cases of compensatory mutations were detected in the TMP binding site of eukaryotic and prokaryotic enzymes. In addition, an intriguing high value of the electric field is reported in the vicinity of the phosphate group of TMP and the putative binding site of the gamma phosphate group of ATP.


    Related Citations: 
    • THYMIDYLATE KINASE OF MYCOBACTERIUM TUBERCULOSIS : A CHIMERA SHARING PROPERTIES COMMON TO EUKARYOTIC AND BACTERIALENZYMES
      Munier-Lehmann, H.,Chaffotte, A.,Labesse, G.,Pochet, S.
      () TO BE PUBLISHED --: --
    • Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis
      Li de la Sierra, I.,Munier-Lehmann, H.,Gilles, A.M.,Barzu, O.,Delarue, M.
      (2000) Acta Crystallogr.,Sect.D 56: 226


    Organizational Affiliation

    Unité de Biochimie Structurale, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE
A
214Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)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 3 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
TMP
Query on TMP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DTKi: 4500 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.622α = 90.00
b = 76.622β = 90.00
c = 134.378γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
CCP4data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance