7CY8 image
Entry Detail
PDB ID:
7CY8
Keywords:
TRANSFERASE
Title:
Crystal Structure of CMD1 in complex with 5mC-DNA and vitamin C
Biological Source:
Source Organism:
Escherichia coli, Chlamydomonas reinhardtii, synthetic construct
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2020-09-03
Release Date:
2020-12-30
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.40 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
7CY8 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
Mutations:D108A, K109A, E198A, N199A, E385A, K388A, D389A
Chain IDs:A
Chain Length:917
Number of Molecules:1
Biological Source:Escherichia coli, Chlamydomonas reinhardtii
UniProt ID:P0AEX9 Pfam ID:PF01547
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*(5CM)P*GP*CP*GP*CP*GP*GP*GP*A)-3')
Chain IDs:B (auth: C), C (auth: D)
Chain Length:14
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
ASC
EDO
FE2
IPA
Primary Citation
Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1.
Nat Commun 12 744 744 (2021)
PMID: 33531488 DOI: 10.1038/s41467-021-21061-2

Abstact

C5-glyceryl-methylcytosine (5gmC) is a novel DNA modification catalyzed by algal TET homologue CMD1 using vitamin C (VC) as co-substrate. Here, we report the structures of CMD1 in apo form and in complexes with VC or/and dsDNA. CMD1 exhibits comparable binding affinities for DNAs of different lengths, structures, and 5mC levels, and displays a moderate substrate preference for 5mCpG-containing DNA. CMD1 adopts the typical DSBH fold of Fe2+/2-OG-dependent dioxygenases. The lactone form of VC binds to the active site and mono-coordinates the Fe2+ in a manner different from 2-OG. The dsDNA binds to a positively charged cleft of CMD1 and the 5mC/C is inserted into the active site and recognized by CMD1 in a similar manner as the TET proteins. The functions of key residues are validated by mutagenesis and activity assay. Our structural and biochemical data together reveal the molecular mechanism for the VC-derived 5gmC DNA modification by CMD1.

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Primary Citation of related structures
7CY8