Journal:IUCrJ:S2052252518018274

A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate

Si Hoon Park, Se Won Suh and Hyun Hyu Song ^[1]

Molecular Tour
Crystal structure of the ternary complex of dCMP hydroxylmethylase from bacteriophage T4 (T4dCH) bound with dCMP and tetrahydrofolate was determined at 1.9 Å resolution. The key residues within T4dCH for accommodating a cofactor without the C-terminal tail, an optimized network of ordered water molecules, and hydrophobic gating mechanism for cofactor regulation were clearly identified.

. THF (orange) and dCMP (green) are drawn as ball and stick models. Oxygen and nitrogen atoms are colored red and blue, respectively. The ligand-recognizing residues are drawn as ball and stick models. Ionic and hydrogen interactions are drawn by dashed lines. Water molecules are shown as red balls.

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. A ribbon diagram showing the ternary complex structure of dimeric T4dCH. The bound dCMP (green) and THF (orange) are drawn using the ball and stick model.

PDB references: apo T4dCH (I-SAD phasing), 6a9b; ternary complex (T4dCH–dCMP–THF), 6a9a.

References

1. ↑ Park SH, Suh SW, Song HK. A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate. IUCrJ. 2019 Jan 24;6(Pt 2):206-217. doi: 10.1107/S2052252518018274. eCollection, 2019 Mar 1. PMID:30867918 doi:http://dx.doi.org/10.1107/S2052252518018274