› 6pbd

X-ray diffraction
2.34Å resolution

DNA N6-Adenine Methyltransferase CcrM In Complex with Double-Stranded DNA Oligonucleotide Containing Its Recognition Sequence GAATC

Released:
DOI: 10.2210/pdb6pbd/pdb
PDB entry 6pbd coloured by chain, front view.
PDB entry 6pbd coloured by chain, side view.
PDB entry 6pbd coloured by chain, top view.
Source organisms:
Primary publication:
The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.
Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X
Nat Commun 10 4600 (2019)
PMID: 31601797

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120446 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA methyltransferase CcrM Chains: A, B
Molecule details ›
Chains: A, B
Length: 366 amino acids
Theoretical weight: 40.74 KDa
Source organism: Caulobacter vibrioides
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CAW2 (Residues: 1-358; Coverage: 100%)
Gene names: CC_0378, ccrM, ccrMIM
Sequence domains:
DNA (5'-D(*CP*GP*AP*TP*TP*CP*AP*AP*TP*GP*AP*AP*TP*CP*CP*CP*AP*AP*G)-3') Chain: X
Molecule details ›
Chain: X
Length: 19 nucleotides
Theoretical weight: 5.8 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*TP*GP*GP*GP*AP*TP*TP*CP*AP*TP*TP*GP*AP*AP*TP*C)-3') Chain: Y
Molecule details ›
Chain: Y
Length: 19 nucleotides
Theoretical weight: 5.85 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SFG 2 x SFG
1 bound ligand:
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 67.683Å b: 117.939Å c: 119.598Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.173 0.208
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 review citations

Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences.
Woodcock et al. (2020)
2 more

4 mentions without citation

The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.
Horton et al. (2019)
3 more