PDBsum entry 1e2k

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Transferase PDB id
Protein chains
308 a.a. *
316 a.a. *
SO4 ×2
TMC ×2
Waters ×364
* Residue conservation analysis
PDB id:
Name: Transferase
Title: 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
Structure: Thymidine kinase. Chain: a, b. Engineered: yes
Source: Herpes simplex virus (type 1/ strain 17). Organism_taxid: 10299. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Homo-Dimer (from PDB file)
1.7Å     R-factor:   0.209     R-free:   0.252
Authors: J.Vogt,L.Scapozza,G.E.Schulz
Key ref:
A.Prota et al. (2000). 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. Biochemistry, 39, 9597-9603. PubMed id: 10924157 DOI: 10.1021/bi000668q
23-May-00     Release date:   19-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03176  (KITH_HHV11) -  Thymidine kinase
376 a.a.
308 a.a.
Protein chain
Pfam   ArchSchema ?
P03176  (KITH_HHV11) -  Thymidine kinase
376 a.a.
316 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Thymidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + thymidine = ADP + thymidine 5'-phosphate
Bound ligand (Het Group name = TMC)
matches with 84.00% similarity
+ thymidine 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     TMP biosynthetic process   1 term 
  Biochemical function     ATP binding     2 terms  


DOI no: 10.1021/bi000668q Biochemistry 39:9597-9603 (2000)
PubMed id: 10924157  
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.
A.Prota, J.Vogt, B.Pilger, R.Perozzo, C.Wurth, V.E.Marquez, P.Russ, G.E.Schulz, G.Folkers, L.Scapozza.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19935678 Z.Chen, H.L.Li, Q.J.Zhang, X.G.Bao, K.Q.Yu, X.M.Luo, W.L.Zhu, and H.L.Jiang (2009).
Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.
  Acta Pharmacol Sin, 30, 1694-1708.  
17302737 L.Egeblad-Welin, Y.Sonntag, H.Eklund, and B.Munch-Petersen (2007).
Functional studies of active-site mutants from Drosophila melanogaster deoxyribonucleoside kinase. Investigations of the putative catalytic glutamate-arginine pair and of residues responsible for substrate specificity.
  FEBS J, 274, 1542-1551.
PDB code: 2jcs
16569849 M.N.Prichard, K.A.Keith, D.C.Quenelle, and E.R.Kern (2006).
Activity and mechanism of action of N-methanocarbathymidine against herpesvirus and orthopoxvirus infections.
  Antimicrob Agents Chemother, 50, 1336-1341.  
14965378 M.Serafini, M.Manganini, G.Borleri, M.Bonamino, L.Imberti, A.Biondi, J.Golay, A.Rambaldi, and M.Introna (2004).
Characterization of CD20-transduced T lymphocytes as an alternative suicide gene therapy approach for the treatment of graft-versus-host disease.
  Hum Gene Ther, 15, 63-76.  
15163659 P.Schelling, M.T.Claus, R.Johner, V.E.Marquez, G.E.Schulz, and L.Scapozza (2004).
Biochemical and structural characterization of (South)-methanocarbathymidine that specifically inhibits growth of herpes simplex virus type 1 thymidine kinase-transduced osteosarcoma cells.
  J Biol Chem, 279, 32832-32838.
PDB code: 1of1
12686543 L.E.Bird, J.Ren, A.Wright, K.D.Leslie, B.Degrève, J.Balzarini, and D.K.Stammers (2003).
Crystal structure of varicella zoster virus thymidine kinase.
  J Biol Chem, 278, 24680-24687.
PDB code: 1osn
  12686722 W.A.Denny (2003).
Prodrugs for Gene-Directed Enzyme-Prodrug Therapy (Suicide Gene Therapy).
  J Biomed Biotechnol, 2003, 48-70.  
11266595 C.Wurth, U.Kessler, J.Vogt, G.E.Schulz, G.Folkers, and L.Scapozza (2001).
The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase.
  Protein Sci, 10, 63-73.
PDB codes: 1e2m 1e2n 1e2p
10985766 L.Mu, S.G.Sarafianos, M.C.Nicklaus, P.Russ, M.A.Siddiqui, H.Ford, H.Mitsuya, R.Le, E.Kodama, C.Meier, T.Knispel, L.Anderson, J.J.Barchi, and V.E.Marquez (2000).
Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase.
  Biochemistry, 39, 11205-11215.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.