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PDBsum entry 2jcs

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2jcs
Jmol
Contents
Protein chains
198 a.a. *
Ligands
TTP ×2
Metals
_MG ×2
Waters ×142
* Residue conservation analysis
PDB id:
2jcs
Name: Transferase
Title: Active site mutant of dnk from d. Melanogaster with dttp bound
Structure: Deoxynucleoside kinase. Chain: a, b. Fragment: residues 1-230. Synonym: deoxyribonucleoside kinase, dm-dnk, multispecific deoxynucleoside kinase. Engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.50Å     R-factor:   0.232     R-free:   0.242
Authors: L.Egeblad-Welin,Y.Sonntag,H.Eklund,B.Munch-Petersen
Key ref: L.Egeblad-Welin et al. (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. PubMed id: 17302737
Date:
03-Jan-07     Release date:   27-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9XZT6  (DNK_DROME) -  Deoxynucleoside kinase
Seq:
Struc:
250 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.145  - Deoxynucleoside kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 2'-deoxynucleoside = ADP + 2'-deoxynucleoside 5'-phosphate
ATP
Bound ligand (Het Group name = TTP)
matches with 76.00% similarity
+ 2'-deoxynucleoside
= ADP
+ 2'-deoxynucleoside 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     nucleobase-containing compound metabolic process   6 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
FEBS J 274:1542-1551 (2007)
PubMed id: 17302737  
 
 
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.
L.Egeblad-Welin, Y.Sonntag, H.Eklund, B.Munch-Petersen.
 
  ABSTRACT  
 
The catalytic reaction mechanism and binding of substrates was investigated for the multisubstrate Drosophila melanogaster deoxyribonucleoside kinase. Mutation of E52 to D, Q and H plus mutations of R105 to K and H were performed to investigate the proposed catalytic reaction mechanism, in which E52 acts as an initiating base and R105 is thought to stabilize the transition state of the reaction. Mutant enzymes (E52D, E52H and R105H) showed a markedly decreased k(cat), while the catalytic activity of E52Q and R105K was abolished. The E52D mutant was crystallized with its feedback inhibitor dTTP. The backbone conformation remained unchanged, and coordination between D52 and the dTTP-Mg complex was observed. The observed decrease in k(cat) for E52D was most likely due to an increased distance between the catalytic carboxyl group and 5'-OH of deoxythymidine (dThd) or deoxycytidine (dCyd). Mutation of Q81 to N and Y70 to W was carried out to investigate substrate binding. The mutations primarily affected the K(m) values, whereas the k(cat) values were of the same magnitude as for the wild-type. The Y70W mutation made the enzyme lose activity towards purines and negative cooperativity towards dThd and dCyd was observed. The Q81N mutation showed a 200- and 100-fold increase in K(m), whereas k(cat) was decreased five- and twofold for dThd and dCyd, respectively, supporting a role in substrate binding. These observations give insight into the mechanisms of substrate binding and catalysis, which is important for developing novel suicide genes and drugs for use in gene therapy.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19343063 C.Hébrard, C.Dumontet, and L.P.Jordheim (2009).
Development of gene therapy in association with clinically used cytotoxic deoxynucleoside analogues.
  Cancer Gene Ther, 16, 541-550.  
18459168 M.J.Pérez-Pérez, E.M.Priego, A.I.Hernández, O.Familiar, M.J.Camarasa, A.Negri, F.Gago, and J.Balzarini (2008).
Structure, physiological role, and specific inhibitors of human thymidine kinase 2 (TK2): present and future.
  Med Res Rev, 28, 797-820.  
18384378 N.E.Mikkelsen, B.Munch-Petersen, and H.Eklund (2008).
Structural studies of nucleoside analog and feedback inhibitor binding to Drosophila melanogaster multisubstrate deoxyribonucleoside kinase.
  FEBS J, 275, 2151-2160.
PDB codes: 2jj8 2vp0 2vp2 2vp4 2vp5 2vp6 2vp9 2vqs
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