› 7eew

X-ray diffraction
2.9Å resolution

Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)

Released:
DOI: 10.2210/pdb7eew/pdb
Model geometry
Fit model/data
PDB entry 7eew coloured by chain, front view.
PDB entry 7eew coloured by chain, side view.
PDB entry 7eew coloured by chain, top view.
Source organisms:
Primary publication:
Structural features of a minimal intact methyltransferase of a type I restriction-modification system.
Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS
Int J Biol Macromol 208 381-389 (2022)
PMID: 35337914

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137265 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
site-specific DNA-methyltransferase (adenine-specific) Chain: A
Molecule details ›
Chain: A
Length: 638 amino acids
Theoretical weight: 71.87 KDa
Source organism: Vibrio vulnificus YJ016
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q7MJG0 (Residues: 1-638; Coverage: 100%)
Gene name: VV2202
Sequence domains:
Protein Ocr Chain: B
Molecule details ›
Chain: B
Length: 117 amino acids
Theoretical weight: 13.82 KDa
Source organism: Escherichia phage T7
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P03775 (Residues: 1-117; Coverage: 100%)
Gene name: 0.3
Sequence domains: DNA mimic ocr

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PAL/PLS BEAMLINE 11C
Spacegroup: P6522
Unit cell:
a: 133.28Å b: 133.28Å c: 236.808Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.273 0.272 0.293
Expression system: Escherichia coli K-12

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