Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex

Hyun Kyu Song, Se Hui Sohn, Se Won Suh

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25 Citations (Scopus)


Bacteriophage T4 deoxycytidylate hydroxymethylase (EC, a homodimer of 246-residue subunits, catalyzes hydroxymethylation of the cytosine base in deoxycytidylate (dCMP) to produce 5-hydroxymethyl-dCMP. It forms part of a phage DNA protection system and appears to function in vivo as a component of a multienzyme complex called deoxyribonucleoside triphosphate (dNTP) synthetase. We have determined its crystal structure in the presence of the substrate dCMP at 1.6 Å resolution. The structure reveals a subunit fold and a dimerization pattern in common with thymidylate synthases, despite low (~ 20%) sequence identity. Among the residues that form the dCMP binding site, those interacting with the sugar and phosphate are arranged in a configuration similar to the deoxyuridylate binding site of thymidylate synthases. However, the residues interacting directly or indirectly with the cytosine base show a more divergent structure and the presumed folate cofactor binding site is more open. Our structure reveals a water molecule properly positioned near C-6 of cytosine to add to the C-7 methylene intermediate during the last step of hydroxymethylation. On the basis of sequence comparison and crystal packing analysis, a hypothetical model for the interaction between T4 deoxycytidylate hydroxymethylase and T4 thymidylate synthase in the dNTP-synthesizing complex has been built.

Original languageEnglish
Pages (from-to)1104-1113
Number of pages10
JournalEMBO Journal
Issue number5
Publication statusPublished - 1999 Mar 1
Externally publishedYes



  • Bacteriophage T4
  • Deoxycytidylate hydroxymethylase
  • Deoxyuridylate hydroxymethylase
  • dNTP-synthesizing complex
  • Thymidylate synthase

ASJC Scopus subject areas

  • Genetics
  • Cell Biology

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