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PDBsum entry 1e2i

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1e2i
Jmol
Contents
Protein chains
300 a.a. *
313 a.a. *
Ligands
SO4 ×2
APS-ARP ×2
Waters ×221
* Residue conservation analysis
PDB id:
1e2i
Name: Transferase
Title: The nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by x-ray crystallography
Structure: Thymidine kinase. Chain: a, b. Engineered: yes
Source: Herpes simplex virus (type 1 / strain 17). Organism_taxid: 10299. Strain: 17. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.222     R-free:   0.273
Authors: J.Vogt,L.Scapozza,G.E.Schulz
Key ref:
J.Vogt et al. (2000). Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography. Proteins, 41, 545-553. PubMed id: 11056041 DOI: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8
Date:
23-May-00     Release date:   06-Nov-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03176  (KITH_HHV11) -  Thymidine kinase
Seq:
Struc:
376 a.a.
300 a.a.
Protein chain
Pfam   ArchSchema ?
P03176  (KITH_HHV11) -  Thymidine kinase
Seq:
Struc:
376 a.a.
313 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.2.7.1.21  - Thymidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + thymidine = ADP + thymidine 5'-phosphate
ATP
+ thymidine
=
ADP
Bound ligand (Het Group name = APS)
matches with 51.00% 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  

 

 
    reference    
 
 
DOI no: 10.1002/1097-0134(20001201)41:4<545::AID-PROT110>3.0.CO;2-8 Proteins 41:545-553 (2000)
PubMed id: 11056041  
 
 
Nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography.
J.Vogt, R.Perozzo, A.Pautsch, A.Prota, P.Schelling, B.Pilger, G.Folkers, L.Scapozza, G.E.Schulz.
 
  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.
 
  Selected figure(s)  
 
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.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20366349 J.I.Sułkowska, P.Sułkowski, and J.N.Onuchic (2009).
Jamming proteins with slipknots and their free energy landscape.
  Phys Rev Lett, 103, 268103.  
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
17658449 S.T.Gammon, M.Bernstein, D.P.Schuster, and D.Piwnica-Worms (2007).
A method for quantification of nucleotides and nucleotide analogues in thymidine kinase assays using lanthanum phosphate coprecipitation.
  Anal Biochem, 369, 80-86.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
16702226 J.Balzarini, S.Liekens, N.Solaroli, K.El Omari, D.K.Stammers, and A.Karlsson (2006).
Engineering of a single conserved amino acid residue of herpes simplex virus type 1 thymidine kinase allows a predominant shift from pyrimidine to purine nucleoside phosphorylation.
  J Biol Chem, 281, 19273-19279.  
17062140 K.El Omari, N.Solaroli, A.Karlsson, J.Balzarini, and D.K.Stammers (2006).
Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design.
  BMC Struct Biol, 6, 22.
PDB code: 2j87
16522804 M.Kotaka, B.Dhaliwal, J.Ren, C.E.Nichols, R.Angell, M.Lockyer, A.R.Hawkins, and D.K.Stammers (2006).
Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding.
  Protein Sci, 15, 774-784.
PDB codes: 2ccg 2ccj 2cck
12454011 A.Haouz, V.Vanheusden, H.Munier-Lehmann, M.Froeyen, P.Herdewijn, S.Van Calenbergh, and M.Delarue (2003).
Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism.
  J Biol Chem, 278, 4963-4971.
PDB codes: 1mrn 1mrs
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
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
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.