Deoxyguanosine kinase

 

Deoxyribonucleoside kinases such as deoxyguanoside kinase (dGK) phosphorylate deoxyribonucleosides. The human form is highly specific for purine substrates. Deoxynucleoside kinases are key targets in chemotherapy of cancer as they are recquired to activate nucleoside analogues by phosphorylation. dGK is involved in the regulation of dGTP and dATP pools, and may have a role in apoptosis.

 

Reference Protein and Structure

Sequence
Q16854 UniProt (2.7.1.76, 2.7.1.113) IPR002624 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
2ocp - Crystal Structure of Human Deoxyguanosine Kinase (2.8 Å) PDBe PDBsum 2ocp
Catalytic CATH Domains
3.40.50.300 CATHdb (see all for 2ocp)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.7.1.113)

2'-deoxyguanosine
CHEBI:17172ChEBI
+
ATP(4-)
CHEBI:30616ChEBI
→
ADP(3-)
CHEBI:456216ChEBI
+
2'-deoxyguanosine 5'-monophosphate(2-)
CHEBI:57673ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: (Dihydroxypropoxymethyl)guanine kinase, 2'-deoxyguanosine kinase, NTP-deoxyguanosine 5'-phosphotransferase, Deoxyguanosine kinase (phosphorylating),

Enzyme Mechanism

Introduction

Activation of the 5'-OH of the deoxyribose by deprotonation with Glu 70 allows a nucleophilic attack of the gamma-phosphate of the phosphate donor. Arg 142 as well as the magnesium cation stabilise the trigonal bypyrimidal transition state formed in the reaction. The magnesium ion will coordinate to the ATP phosphate groups however exact Mg2+ ligand positions have not been identified across deoxynucleoside kinases.

Catalytic Residues Roles

UniProt PDB* (2ocp)
Glu70 Glu70(34)A Acts as a general base, deprotonating the 5'OH group of the nucleoside. activator, proton acceptor, proton donor
Arg142 Arg142(106)A Positions Glu 70 by forming hydrogen bonds and also stabilises the negative charges from the transition state in the reaction. hydrogen bond donor, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic substitution, overall reactant used, overall product formed, inferred reaction step, native state of enzyme regenerated

References

  1. Eriksson S et al. (2002), Cell Mol Life Sci, 59, 1327-1346. Structure and function of cellular deoxyribonucleoside kinases. DOI:10.1007/s00018-002-8511-x. PMID:12363036.
  2. Egeblad-Welin L et al. (2007), FEBS J, 274, 1542-1551. 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. DOI:10.1111/j.1742-4658.2007.05701.x. PMID:17302737.
  3. Sandrini MP et al. (2005), Trends Biochem Sci, 30, 225-228. Deoxyribonucleoside kinases: two enzyme families catalyze the same reaction. DOI:10.1016/j.tibs.2005.03.003. PMID:15896737.
  4. Wang L et al. (2003), FEBS Lett, 554, 319-322. Mitochondrial deoxyguanosine kinase mutations and mitochondrial DNA depletion syndrome. DOI:10.1016/s0014-5793(03)01181-5. PMID:14623087.

Step 1. Glu70 acts as an initiating base to increase nucleophilicity of the 5' OH on the substrate. The 5' OH then attacks the gamma phosphate on ATP.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg142(106)A electrostatic stabiliser
Glu70(34)A activator
Arg142(106)A hydrogen bond donor
Glu70(34)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, overall product formed

Step 2. Glu70 is deprotonated, ready for another round of catalysis.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg142(106)A hydrogen bond donor
Glu70(34)A proton donor

Chemical Components

inferred reaction step, proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu70 acts as an initiating base to increase nucleophilicity of the 5' OH on the substrate. The 5' OH then attacks the gamma phosphate on ATP.

Step 2. Glu70 is deprotonated, ready for another round of catalysis.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, Morwenna Hall