1VTK

THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


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Literature

The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.

Wild, K.Bohner, T.Folkers, G.Schulz, G.E.

(1997) Protein Sci 6: 2097-2106

  • DOI: 10.1002/pro.5560061005
  • Primary Citation of Related Structures:  
    3VTK, 2VTK, 1VTK

  • PubMed Abstract: 
  • Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2 ...

    Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 A3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well-known nucleoside monophosphate kinases but contains large additional peptide segments.


    Related Citations: 
    • The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1
      Wild, K., Bohner, T., Aubry, A., Folkers, G., Schulz, G.E.
      (1995) FEBS Lett 368: 289
    • A Fast Method for Obtaining Highly Pure Recombinant Herpes Simplex Virus Type 1 Thymidine Kinase
      Fetzer, J., Michael, M., Bohner, T., Hofbauer, R., Folkers, G.
      (1994) Protein Expr Purif 5: 432

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDINE KINASEA343Human alphaherpesvirus 1 strain FMutation(s): 0 
EC: 2.7.1.21
UniProt
Find proteins for P0DTH5 (Human herpesvirus 1 (strain 17))
Explore P0DTH5 
Go to UniProtKB:  P0DTH5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
TMP (Subject of Investigation/LOI)
Query on TMP

Download Ideal Coordinates CCD File 
C [auth A]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.4α = 90
b = 83.4β = 90
c = 156.7γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 1997-04-01 
  • Released Date: 1997-10-22 
  • Deposition Author(s): Wild, K., Schulz, G.E.

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance