6A9A

Ternary complex crystal structure of dCH with dCMP and THF

Summary for 6A9A

• Entry DOI: 10.2210/pdb6a9a/pdb
• Descriptor: Deoxycytidylate 5-hydroxymethyltransferase, IODIDE ION, 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, ... (5 entities in total)
• Functional Keywords: pyrimidine hydroxymethylase, transferase
• Biological source: Enterobacteria phage T4 (Bacteriophage T4)
• Total number of polymer chains: 1
• Total formula weight: 29385.71

Authors

Park, S.H.,Song, H.K. (deposition date: 2018-07-12, release date: 2019-01-02, Last modification date: 2023-11-22)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.9 Å)