1B49

DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND)

1B49 の概要

• エントリーDOI: 10.2210/pdb1b49/pdb
• 分子名称: PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE), PHOSPHATE ION (3 entities in total)
• 機能のキーワード: hydroxymethylase, dntp synthesizing complex, transferase
• 由来する生物種: Enterobacteria phage T4
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 57236.40

構造登録者

Song, H.K.,Sohn, S.H.,Suh, S.W. (登録日: 1999-01-06, 公開日: 1999-01-13, 最終更新日: 2024-02-07)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.3 Å)