› 5hr4

X-ray diffraction
2.6Å resolution

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering of new specificities

Released:
DOI: 10.2210/pdb5hr4/pdb
PDB entry 5hr4 coloured by chain, front view.
PDB entry 5hr4 coloured by chain, side view.
PDB entry 5hr4 coloured by chain, top view.
Source organism: Methylophilus methylotrophus
Primary publication:
Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.
Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK
OpenAccess logo PLoS Biol 14 e1002442 (2016)
PMID: 27082731

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109687 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
site-specific DNA-methyltransferase (adenine-specific) Chains: C, J
Molecule details ›
Chains: C, J
Length: 919 amino acids
Theoretical weight: 105.26 KDa
Source organism: Methylophilus methylotrophus
Expression system: Escherichia coli
UniProt:
  • Canonical: B2MU09 (Residues: 1-919; Coverage: 100%)
Gene name: mmeIRM
Sequence domains:
DNA (5'-D(P*TP*AP*TP*CP*CP*GP*AP*CP*AP*TP*AP*AP*C)-3') Chains: H, K
Molecule details ›
Chains: H, K
Length: 13 nucleotides
Theoretical weight: 3.92 KDa
Source organism: Methylophilus methylotrophus
Expression system: Not provided
DNA (5'-D(P*GP*TP*TP*AP*TP*GP*TP*CP*GP*GP*AP*TP*A)-3') Chains: I, L
Molecule details ›
Chains: I, L
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Methylophilus methylotrophus
Expression system: Not provided

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P1
Unit cell:
a: 61.877Å b: 95.292Å c: 161.969Å
α: 72.84° β: 89.15° γ: 71.62°
R-values:
R R work R free
0.216 0.215 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Engineering altered protein-DNA recognition specificity.
Bogdanove et al. (2018)
1 more

1 mention without citation

Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria.
Papoulis et al. (2021)