› 5ybb

X-ray diffraction
3.2Å resolution

Structural basis underlying complex assembly andconformational transition of the type I R-M system

Released:
DOI: 10.2210/pdb5ybb/pdb
PDB entry 5ybb coloured by chain, front view.
PDB entry 5ybb coloured by chain, side view.
PDB entry 5ybb coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Primary publication:
Structural basis underlying complex assembly and conformational transition of the type I R-M system.
Liu YP, Tang Q, Zhang JZ, Tian LF, Gao P, Yan XX
Proc Natl Acad Sci U S A 114 11151-11156 (2017)
PMID: 28973912

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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119429 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
site-specific DNA-methyltransferase (adenine-specific) Chains: A, B, C, E
Molecule details ›
Chains: A, B, C, E
Length: 507 amino acids
Theoretical weight: 58.57 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q8R9Q4 (Residues: 1-507; Coverage: 100%)
Gene names: HsdM, TTE1547
Sequence domains:
Structure domains: Vaccinia Virus protein VP39
Type I restriction modification DNA specificity domain-containing protein Chains: D, G
Molecule details ›
Chains: D, G
Length: 398 amino acids
Theoretical weight: 44.72 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q8R9Q6 (Residues: 2-398; Coverage: 100%)
Gene names: HsdS, TTE1545
Sequence domains: Type I restriction modification DNA specificity domain
DNA Chain: H
Molecule details ›
Chain: H
Length: 22 nucleotides
Theoretical weight: 6.83 KDa
DNA Chain: I
Molecule details ›
Chain: I
Length: 22 nucleotides
Theoretical weight: 6.67 KDa

Ligands and Environments


Cofactor: Ligand SAM 2 x SAM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P41
Unit cell:
a: 121.6Å b: 121.6Å c: 280.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.236 0.272
Expression system: Escherichia coli K-12

Quick links

Citations

1 review citation

Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria.
Gao et al. (2023)
9 other articles

2 mentions without citation

Structural basis underlying complex assembly and conformational transition of the type I R-M system.
Liu et al. (2017)
1 more