1E2N

HPT + HMTT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Effect of Substrate Binding on the Conformation and Structural Stability of Herpes Simplex Virus Type 1 Thymidine Kinase

Wurth, C.Kessler, U.Vogt, J.Schulz, G.E.Folkers, G.Scapozza, L.

(2001) Protein Sci. 10: 63

  • DOI: 10.1110/ps.27401
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of Herpes simplex virus type 1 thymidine kinase (TK(HSV1)) is known at high resolution in complex with a series of ligands and exhibits important structural similarities to the nucleoside monophosphate (NMP) kinase family, which are kno ...

    The structure of Herpes simplex virus type 1 thymidine kinase (TK(HSV1)) is known at high resolution in complex with a series of ligands and exhibits important structural similarities to the nucleoside monophosphate (NMP) kinase family, which are known to show large conformational changes upon binding of substrates. The effect of substrate binding on the conformation and structural stability of TK(HSV1), measured by thermal denaturation experiments, far-UV circular dichroism (CD) and fluorescence is described, and the results indicate that the conformation of the ligand-free TK(HSV1) is less ordered and less stable compared to the ligated enzyme. Furthermore, two crystal structures of TK(HSV1) in complex with two new ligands, HPT and HMTT, refined to 2.2 A are presented. Although TK(HSV1):HPT does not exhibit any significant deviations from the model of TK(HSV1):dT, the TK(HSV1):HMTT complex displays a unique conformationally altered active site resulting in a lowered thermal stability of this complex. Moreover, we show that binding affinity and binding mode of the ligand correlate with thermal stability of the complex. We use this correlation to propose a method to estimate binding constants for new TK(HSV1)substrates using thermal denaturation measurements monitored by CD spectroscopy. The kinetic and structural results of both test substrates HPT and HMTT show that the CD thermal denaturation system is very sensitive to conformational changes caused by unusual binding of a substrate analog.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Department of Applied BioSciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, CH-8057 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
RCA
Query on RCA

Download SDF File 
Download CCD File 
A, B
6-{[4-(HYDROXYMETHYL)-5-METHYL-2,6-DIOXOHEXAHYDROPYRIMIDIN-5-YL]METHYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
HYDROXYMETHYL-HYDROTHYMYL-THYMINE; 5-[THYMIN-6-YL]METHYL-6-HYDRO-6-HYDROXYMETHYL-THYMINE
C12 H16 N4 O5
KBBKHMIEEMSXSM-JVXZTZIISA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RCAKi: 30900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 113.600α = 90.00
b = 118.800β = 90.00
c = 108.500γ = 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: 2001-03-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance