6A9B

T4 dCMP hydroxymethylase structure solved by I-SAD using a home source

6A9B の概要

• エントリーDOI: 10.2210/pdb6a9b/pdb
• 関連するPDBエントリー: 6A9A
• 分子名称: Deoxycytidylate 5-hydroxymethyltransferase, IODIDE ION, PHOSPHATE ION, ... (4 entities in total)
• 機能のキーワード: pyrimidine hydroxymethylase, transferase
• 由来する生物種: Enterobacteria phage T4 (Bacteriophage T4)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 28745.10

構造登録者

Park, S.H.,Song, H.K. (登録日: 2018-07-12, 公開日: 2019-01-02, 最終更新日: 2024-03-27)

主引用文献

Park, S.H.,Suh, S.W.,Song, H.K.
A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate.
Iucrj, 6:206-217, 2019

PubMed Abstract: To protect viral DNA against the host bacterial restriction system, bacterio-phages utilize a special modification system - hydroxymethylation - in which dCMP hydroxymethylase (dCH) converts dCMP to 5-hydroxymethyl-dCMP (5hm-dCMP) using 5,10-methylenetetrahydrofolate as a cofactor. Despite shared similarity with thymidylate synthase (TS), dCH catalyzes hydroxylation through an exocyclic methylene intermediate during the last step, which is different from the hydride transfer that occurs with TS. In contrast to the extensively studied TS, the hydroxymethylation mechanism of a cytosine base is not well understood due to the lack of a ternary complex structure of dCH in the presence of both its substrate and cofactor. This paper reports the crystal structure of the ternary complex of dCH from bacteriophage T4 (T4dCH) with dCMP and tetrahydrofolate at 1.9 Å resolution. The authors found key residues of T4dCH for accommodating the cofactor without a C-terminal tail, an optimized network of ordered water molecules and a hydrophobic gating mechanism for cofactor regulation. In combination with biochemical data on structure-based mutants, key residues within T4dCH and a substrate water molecule for hydroxymethylation were identified. Based on these results, a complete enzyme mechanism of dCH and signature residues that can identify dCH enzymes within the TS family have been proposed. These findings provide a fundamental basis for understanding the pyrimidine modification system.

PubMed: 30867918
DOI: 10.1107/S2052252518018274

実験手法

X-RAY DIFFRACTION (2.01 Å)