PDBsum entry 1e2j

Transferase

PDB id: 1e2j

Contents

Protein chains

306 a.a. *

Ligands

SO4 ×2

THM ×2

Waters ×111

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by x-Ray crystallography.

Authors

J.Vogt, R.Perozzo, A.Pautsch, A.Prota, P.Schelling, B.Pilger, G.Folkers, L.Scapozza, G.E.Schulz.

Ref.

Proteins, 2000, 41, 545-553. [DOI no: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8]

PubMed id

11056041

Abstract

The crystal structures of the full-length Herpes simplex virus type 1 thymidine kinase in its unligated form and in a complex with an adenine analogue have been determined at 1.9 A resolution. The unligated enzyme contains four water molecules in the thymidine pocket and reveals a small induced fit on substrate binding. The structure of the ligated enzyme shows for the first time a bound adenine analogue after numerous complexes with thymine and guanine analogues have been reported. The adenine analogue constitutes a new lead compound for enzyme-prodrug gene therapy. In addition, the structure of mutant Q125N modifying the binding site of the natural substrate thymidine in complex with this substrate has been established at 2.5 A resolution. It reveals that neither the binding mode of thymidine nor the polypeptide backbone conformation is altered, except that the two major hydrogen bonds to thymidine are replaced by a single water-mediated hydrogen bond, which improves the relative acceptance of the prodrugs aciclovir and ganciclovir compared with the natural substrate. Accordingly, the mutant structure represents a first step toward improving the virus-directed enzyme-prodrug gene therapy by enzyme engineering.

Figure 3.
Figure 3. Structural formulae of the adenosine analogue 9-(2-(S)-hydroxypropyl)adenine (HPA) and the AMP analogue 9-(2-phosphonylmethoxyethyl)adenine (PMEA). HPA was used as a racemic mixture.

Figure 6.
Figure 6. Superposition of mutant TK[HSV1](Q125N) in complex with dT (thick solid lines, C atoms marked by small dots, hydrogen bonds are dotted) with wild-type TK[HSV1] in complex with aciclovir (thin solid lines),[19] ganciclovir (thin dotted lines)[19]and dT (thick dotted lines).[19] For sake of clarity, side chains are only drawn for TK[HSV1](Q125N):dT and TK[HSV1]:aciclovir. Water molecules and hydrogen bonds are depicted for TK[HSV1](Q125N):dT (black circles) and TK[HSV1]:aciclovir (pale circles). For aciclovir, only the location of the hydroxyl group at the 5 -OH position of dT is shown.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2000, 41, 545-553) copyright 2000.

Secondary reference #1

Title

The three-Dimensional structure of thymidine kinase from herpes simplex virus type 1.

Authors

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

Ref.

FEBS Lett, 1995, 368, 289-292. [DOI no: 10.1016/0014-5793(95)00680-8]

PubMed id

7628623

Figure 1.
Fig. 1. Sketch of the chain fold of thymidine kinase from Herpes simplex virus type 1. To avoid crossovers the sketch is somewhat sim- plified rendering some helix positions disputable. All ,B-strands (quad- rangles) run towards the viewer, the orientations of the helices (circles) are indicated by the arrows. Dashed lines denote chain segments that are not yet modeled. The central residues of secondary structure ele- ments bl, b2, b3, b4, b5, al, a, a3 a4, a5, a6, a7, a8, a9, al0, al 1, and a12 are 52, 79, 159, 203, 326, 67, 87, 103, 131, 72, 190, 215, 239, 292, 314, 340, and 364, respectively.

Figure 2.
Fig. 2. Stereo-view of the current a-backbone of dimeric thymidine kinase from Herpes simplex virus type 1 with numbering and the bound substrates thymidine and ATP. The dashed lines indicate regions of low density which have not yet been modeled. The chosen orientation emphasizes the planarity of the interface. The two-fold axis runs from the lefthand side in the front to the right hand side in the rear.

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #2

Title

Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir.

Authors

D.G.Brown, R.Visse, G.Sandhu, A.Davies, P.J.Rizkallah, C.Melitz, W.C.Summers, M.R.Sanderson.

Ref.

Nat Struct Biol, 1995, 2, 876-881.

PubMed id

7552712