› 7l4c

X-ray diffraction
2.11Å resolution

Crystal structure of the DRM2-CTT DNA complex

Released:
DOI: 10.2210/pdb7l4c/pdb
PDB entry 7l4c coloured by chain, front view.
PDB entry 7l4c coloured by chain, side view.
PDB entry 7l4c coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Substrate deformation regulates DRM2-mediated DNA methylation in plants.
Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J
OpenAccess logo Sci Adv 7 (2021)
PMID: 34078593

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121521 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase DRM2 Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 40.21 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9M548 (Residues: 274-626; Coverage: 56%)
Gene names: At5g14620/At5g14630, DRM2, T15N1.110/T15N1.120
Sequence domains: C-5 cytosine-specific DNA methylase
DNA (5'-D(*TP*AP*AP*AP*TP*TP*AP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 18 nucleotides
Theoretical weight: 5.55 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
DNA (5'-D(*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*TP*AP*AP*TP*TP*TP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand GOL 1 x GOL
1 modified residue:
Ligand C49 1 x C49

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: C2221
Unit cell:
a: 54.376Å b: 232.512Å c: 117.789Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.215
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Epigenetic regulation during meiosis and crossover.
Chowdary et al. (2023)
8 other articles

3 mentions without citation

Mechanistic basis for maintenance of CHG DNA methylation in plants.
Fang et al. (2022)
2 more