7VPN

Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain in complex with Mn(II) and N-Oxalylglycine

Summary for 7VPN

• Entry DOI: 10.2210/pdb7vpn/pdb
• Descriptor: CcTet molecule, MANGANESE (II) ION, N-OXALYLGLYCINE, ... (4 entities in total)
• Functional Keywords: dioxygenase, 5-methylcytosine oxidation, n6-methyldeoxyadenine demethylation, dna binding protein
• Biological source: Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (Inky cap fungus, Hormographiella aspergillata)
• Total number of polymer chains: 4
• Total formula weight: 192838.75

Authors

Mu, Y.J.,Zhang, L.,Zhang, L. (deposition date: 2021-10-17, release date: 2022-03-30, Last modification date: 2023-11-29)

Primary citation

Mu, Y.,Zhang, L.,Hu, J.,Zhou, J.,Lin, H.W.,He, C.,Chen, H.Z.,Zhang, L.
A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Nat.Chem.Biol., 18:733-741, 2022

PubMed Abstract: N-methyladenosine (6mA) is a DNA modification that has recently been found to play regulatory roles during mammalian early embryo development and mitochondrial transcription. We found that a dioxygenase CcTet from the fungus Coprinopsis cinerea is also a dsDNA 6mA demethylase. It oxidizes 6mA to the intermediate N-hydroxymethyladenosine (6hmA) with robust activity of 6mA-containing duplex DNA (dsDNA) as well as isolated genomics DNA. Structural characterization revealed that CcTet utilizes three flexible loop regions and two key residues-D337 and G331-in the active pocket to preferentially recognize substrates on dsDNA. A CcTet D337F mutant protein retained the catalytic activity on 6mA but lost activity on 5-methylcytosine. Our findings uncovered a 6mA demethylase that works on dsDNA, suggesting potential 6mA demethylation in fungi and elucidating 6mA recognition and the catalytic mechanism of CcTet. The CcTet D337F mutant protein also provides a chemical biology tool for future functional manipulation of DNA 6mA in vivo.

PubMed: 35654845
DOI: 10.1038/s41589-022-01041-3

Experimental method

X-RAY DIFFRACTION (2.6 Å)