Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 46.54 kDa 
• Atom Count: 3171 
• Residue Count: 392 
• Unique protein chains: 1

1W2H

Crystal Structure Of Mycobacterium Tuberculosis Thymidylate Kinase Complexed With Azidothymidine Monophosphate (AZT-MP) (2.0 A Resolution)

• DOI: 10.2210/pdb1W2H/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-06 Released: 2005-01-12 
• Deposition Author(s): Fioravanti, E., Adam, V., Munier-Lehmann, H., Bourgeois, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.296 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 

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: 130-137

• PubMed: 15628853 
• DOI: 10.1021/bi0484163
• Primary Citation of Related Structures:  
  1W2H, 1W2G


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE KINASE TMK	A, B	214	Mycobacterium tuberculosis	Mutation(s): 0  EC: 2.7.4.9
Find proteins for P9WKE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKE1  Go to UniProtKB:  P9WKE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATM	A, B	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P OIFWQOKDSPDILA-XLPZGREQSA-N
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ATM	Ki:  10000   nM  Binding MOAD
ATM	Ki :  10000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.296 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.521	α = 90
b = 64.521	β = 90
c = 195.366	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-06 
• Released Date: 2005-01-12 
Deposition Author(s): Fioravanti, E., Adam, V., Munier-Lehmann, H., Bourgeois, D.

Revision History 

• Version 1.0: 2005-01-12
  Type: Initial release
  
• Version 1.1: 2011-06-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-19
  Changes: Atomic model, Data collection, Database references, Derived calculations