Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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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

  • DOI: https://doi.org/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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (THYMIDYLATE KINASE)213Escherichia coliMutation(s): 0 
Find proteins for P0A720 (Escherichia coli (strain K12))
Explore P0A720 
Go to UniProtKB:  P0A720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A720
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on Z5A

Download Ideal Coordinates CCD File 
C20 H24 N10 O22 P5
Binding Affinity Annotations 
IDSourceBinding Affinity
Z5A Binding MOAD:  5TMP Kd: 34 (nM) from 1 assay(s)
PDBBind:  5TMP Kd: 34 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 152.1α = 90
b = 152.1β = 90
c = 75.6γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations