8C58

CpG specific M.MpeI methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA

Summary for 8C58

• Entry DOI: 10.2210/pdb8c58/pdb
• Related: 4DA4 4DKJ 8C56 8C57 8C59
• Descriptor: Cytosine-specific methyltransferase, DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5OC)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)
• Functional Keywords: m.mpei, dna methyltransferase, dna, 5-methylcytosine, 5-hydroxycytosine, 5mc, 5ohc, cpg, transferase
• Biological source: Malacoplasma penetrans HF-2; More
• Total number of polymer chains: 3
• Total formula weight: 56025.75

Authors

Wojciechowski, M.,Czapinska, H.,Krwawicz, J.,Rafalski, D.,Bochtler, M. (deposition date: 2023-01-06, release date: 2024-01-17, Last modification date: 2024-09-04)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)