1E2P

Thymidine kinase, DHBT

DOI: 10.2210/pdb1E2P/pdb

Classification: TRANSFERASE
Organism(s): Human alphaherpesvirus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-05-23 Released: 2001-04-26
Deposition Author(s): Schulz, G.E., Kessler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.261
R-Value Work: 0.209

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

PubMed: 11266595 Search on PubMedSearch on PubMed Central
DOI: 10.1110/ps.27401
Primary Citation of Related Structures:
1E2P, 1E2N, 1E2M

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 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:

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 Biol 2: 876

Organizational Affiliation:

Department of Applied BioSciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, CH-8057 Zürich, Switzerland.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE KINASE	A, B	331	Human alphaherpesvirus 1	Mutation(s): 0 EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17)) Explore P03176 Go to UniProtKB: P03176
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CCV Query on CCV Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain F [B] MOL2 format, chain D [A] MOL2 format, chain F [B]	A, B	6-[3-HYDROXY-2-(HYDROXYMETHYL)PROPYL]-5-METHYL-2,4(1H,3H)-PYRIMIDINEDIONE C₉ H₁₄ N₂ O₄ CLCPDSJUXHDRGX-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain E [B] MOL2 format, chain C [A] MOL2 format, chain E [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction