Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 24.72 kDa 
• Atom Count: 1884 
• Modelled Residue Count: 210 
• Deposited Residue Count: 213 
• Unique protein chains: 1

4TMK

COMPLEX OF E. COLI THYMIDYLATE KINASE WITH THE BISUBSTRATE INHIBITOR TP5A

• PDB DOI: 10.2210/pdb4TMK/pdb

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


• Deposited: 1998-08-31 Released: 1998-11-25 
• Deposition Author(s): Lavie, A., Ostermann, N., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.

Lavie, A., Ostermann, N., Brundiers, R., Goody, R.S., Reinstein, J., Konrad, M., Schlichting, I.

(1998) Proc Natl Acad Sci U S A 95: 14045-14050

• PubMed: 9826650 
• DOI: 10.1073/pnas.95.24.14045
• Primary Citation of Related Structures:  
  4TMK, 5TMP


• PubMed Abstract: 
  

The crystal structures of Escherichia coli thymidylate kinase (TmpK) in complex with P1-(5'-adenosyl)-P5-(5'-thymidyl)pentaphosphate and P1-(5'-adenosyl)P5-[5'-(3'-azido-3'-deoxythymidine)] pentaphosphate have been solved to 2.0-A and 2.2-A resolution, respectively. The overall structure of the bacterial TmpK is very similar to that of yeast TmpK. In contrast to the human and yeast TmpKs, which phosphorylate 3'-azido-3'-deoxythymidine 5'-monophosphate (AZT-MP) at a 200-fold reduced turnover number (kcat) in comparison to the physiological substrate dTMP, reduction of kcat is only 2-fold for the bacterial enzyme. The different kinetic properties toward AZT-MP between the eukaryotic TmpKs and E. coli TmpK can be rationalized by the different ways in which these enzymes stabilize the presumed transition state and the different manner in which a carboxylic acid side chain in the P loop interacts with the deoxyribose of the monophosphate. Yeast TmpK interacts with the 3'-hydroxyl of dTMP through Asp-14 of the P loop in a bidentate manner: binding of AZT-MP results in a shift of the P loop to accommodate the larger substituent. In E. coli TmpK, the corresponding residue is Glu-12, and it interacts in a side-on fashion with the 3'-hydroxyl of dTMP. This different mode of interaction between the P loop carboxylic acid with the 3' substituent of the monophosphate deoxyribose allows the accommodation of an azido group in the case of the E. coli enzyme without significant P loop movement. In addition, although the yeast enzyme uses Arg-15 (a glycine in E. coli) to stabilize the transition state, E. coli seems to use Arg-153 from a region termed Lid instead. Thus, the binding of AZT-MP to the yeast TmpK results in the shift of a catalytic residue, which is not the case for the bacterial kinase.

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Organizational Affiliation: 

Department of Physical Biochemistry, Max Planck Institute for Molecular Physiology, Rheinlanddamm 201, 44139 Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (THYMIDYLATE KINASE)	A	213	Escherichia coli	Mutation(s): 0  EC: 2.7.4.9
UniProt
Find proteins for P0A720 (Escherichia coli (strain K12)) Explore P0A720  Go to UniProtKB:  P0A720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T5A	B [auth A]	P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE C20 H30 N7 O23 P5 JCFDSPQTEMXXLO-SLFMBYJQSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
T5A	Binding MOAD:  4TMK	Kd: 20 (nM) from 1 assay(s)
	PDBBind:  4TMK	Kd: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.7	α = 90
b = 151.7	β = 90
c = 74.48	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
DM	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-31 
• Released Date: 1998-11-25 
Deposition Author(s): Lavie, A., Ostermann, N., Schlichting, I.

Revision History  

• Version 1.0: 1998-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance