1E2K

Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kinetics and Crystal Structure of the Wild-Type and the Engineered Y101F Mutant of Herpes Simplex Virus Type 1 Thymidine Kinase Interacting with (North)-Methanocarba-Thymidine

Prota, A.Vogt, J.Pilger, B.Perozzo, R.Wurth, C.Marquez, V.Russ, P.Schulz, G.E.Folkers, G.Scapozza, L.

(2000) Biochemistry 39: 9597

  • Primary Citation of Related Structures:  1E2L

  • PubMed Abstract: 
  • Kinetic and crystallographic analyses of wild-type Herpes simplex virus type 1 thymidine kinase (TK(HSV1)) and its Y101F-mutant [TK(HSV1)(Y101F)] acting on the potent antiviral drug 2'-exo-methanocarba-thymidine (MCT) have been performed. The kinetic ...

    Kinetic and crystallographic analyses of wild-type Herpes simplex virus type 1 thymidine kinase (TK(HSV1)) and its Y101F-mutant [TK(HSV1)(Y101F)] acting on the potent antiviral drug 2'-exo-methanocarba-thymidine (MCT) have been performed. The kinetic study reveals a 12-fold K(M) increase for thymidine processed with Y101F as compared to the wild-type TK(HSV1). Furthermore, MCT is a substrate for both wild-type and mutant TK(HSV1). Its binding affinity for TK(HSV1) and TK(HSV1)(Y101F), expressed as K(i), is 11 microM and 51 microM, respectively, whereas the K(i) for human cytosolic thymidine kinase is as high as 1.6 mM, rendering TK(HSV1) a selectivity filter for antiviral activity. Moreover, TK(HSV1)(Y101F) shows a decrease in the quotient of the catalytic efficiency (k(cat)/K(M)) of dT over MCT corresponding to an increased specificity for MCT when compared to the wild-type enzyme. Crystal structures of wild-type and mutant TK(HSV1) in complex with MCT have been determined to resolutions of 1.7 and 2.4 A, respectively. The thymine moiety of MCT binds like the base of dT while the conformationally restricted bicyclo[3.1.0]hexane, mimicking the sugar moiety, assumes a 2'-exo envelope conformation that is flatter than the one observed for the free compound. The hydrogen bond pattern around the sugar-like moiety differs from that of thymidine, revealing the importance of the rigid conformation of MCT with respect to hydrogen bonds. These findings make MCT a lead compound in the design of resistance-repellent drugs for antiviral therapy, and mutant Y101F, in combination with MCT, opens new possibilities for gene therapy.


    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
    • Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir
      Brown, D.G.,Visse, R.,Sandhu, G.,Davies, A.,Rizkallah, P.J.,Melitz, C.,Summers, W.C.,Sanderson, M.R.
      (1995) Nat.Struct.Mol.Biol. 2: 876


    Organizational Affiliation

    Department of Applied BioSciences, Swiss Federal Institute of Technology (ETH), Z├╝rich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE KINASE
A, B
331Human herpesvirus 1 (strain 17)Gene Names: TK
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Go to UniProtKB:  P03176
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TMC
Query on TMC

Download SDF File 
Download CCD File 
A, B
1-[4-HYDROXY-5-(HYDROXYMETHYL)BICYCLO[3.1.0]HEX-2-YL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
(N)-METHANOCARBA-THYMIDINE
C12 H16 N2 O4
NOWRLNPOENZFHP-ARHDFHRDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TMCKi: 11400 nM BINDINGMOAD
TMCKi: 11400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.209 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 114.000α = 90.00
b = 117.700β = 90.00
c = 108.200γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance