1B5D

DCMP Hydroxymethylase from T4 (Intact)

Summary for 1B5D

• Entry DOI: 10.2210/pdb1b5d/pdb
• Descriptor: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE), 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: hydroxymethylase, dntp synthesizing complex, transferase
• Biological source: Enterobacteria phage T4
• Total number of polymer chains: 2
• Total formula weight: 57660.85

Authors

Song, H.K.,Sohn, S.H.,Suh, S.W. (deposition date: 1999-01-06, release date: 1999-01-13, Last modification date: 2024-02-07)

Primary citation

Song, H.K.,Sohn, S.H.,Suh, S.W.
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
EMBO J., 18:1104-1113, 1999

PubMed Abstract: Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), 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 A resolution. The structure reveals a subunit fold and a dimerization pattern in common with thymidylate synthases, despite low (approximately 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.

PubMed: 10064578
DOI: 10.1093/emboj/18.5.1104

Experimental method

X-RAY DIFFRACTION (2.2 Å)