8C57

CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) and 5-methylcytosine containing dsDNA

8C57 の概要

• エントリーDOI: 10.2210/pdb8c57/pdb
• 関連するPDBエントリー: 4DA4 4DKJ 8C56 8C58 8C59
• 分子名称: Cytosine-specific methyltransferase, DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5MA)P*GP*CP*TP*GP*AP*A)-3'), DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3'), ... (7 entities in total)
• 機能のキーワード: m.mpei, dna methyltransferase, dna, 5-methylcytosine, 5-methyl-5, 6-dihydro-5-azacytosine, 5mc, dhac, cpg, transferase
• 由来する生物種: Malacoplasma penetrans HF-2; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 55934.69

構造登録者

Wojciechowski, M.,Czapinska, H.,Krwawicz, J.,Rafalski, D.,Bochtler, M. (登録日: 2023-01-06, 公開日: 2024-01-17, 最終更新日: 2024-09-04)

主引用文献

Wojciechowski, M.,Czapinska, H.,Krwawicz, J.,Rafalski, D.,Bochtler, M.
Cytosine analogues as DNA methyltransferase substrates.
Nucleic Acids Res., 52:9267-9281, 2024

PubMed Abstract: DNA methyltransferases are drug targets for myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML), acute myelogenous leukemia (AML) and possibly β-hemoglobinopathies. We characterize the interaction of nucleoside analogues in DNA with a prokaryotic CpG-specific DNA methyltransferase (M.MpeI) as a model for mammalian DNMT1 methyltransferases. We tested DNA containing 5-hydroxymethylcytosine (5hmC), 5-hydroxycytosine (5OHC), 5-methyl-2-pyrimidinone (in the ribosylated form known as 5-methylzebularine, 5mZ), 5,6-dihydro-5-azacytosine (dhaC), 5-fluorocytosine (5FC), 5-chlorocytosine (5ClC), 5-bromocytosine (5BrC) and 5-iodocytosine (5IC). Covalent complex formation was by far most efficient for 5FC. Non-covalent complexes were most abundant for dhaC and 5mZ. Surprisingly, we observed methylation of 5IC and 5BrC, and to a lesser extent 5ClC and 5FC, in the presence, but not the absence of small molecule thiol nucleophiles. For 5IC and 5BrC, we demonstrated by mass spectrometry that the reactions were due to methyltransferase driven dehalogenation, followed by methylation. Crystal structures of M.MpeI-DNA complexes capture the 'in' conformation of the active site loop for analogues with small or rotatable (5mZ) 5-substituents and its 'out' form for bulky 5-substituents. Since very similar 'in' and 'out' loop conformations were also observed for DNMT1, it is likely that our conclusions generalize to other DNA methyltransferases.

PubMed: 38966999
DOI: 10.1093/nar/gkae568

実験手法

X-RAY DIFFRACTION (1.95 Å)