› 5ffj

X-ray diffraction
2.84Å resolution

Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme LlaGI in complex with a DNA substrate mimic

Released:
DOI: 10.2210/pdb5ffj/pdb
PDB entry 5ffj coloured by chain, front view.
PDB entry 5ffj coloured by chain, side view.
PDB entry 5ffj coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.
Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD, Saikrishnan K
Nucleic Acids Res 44 4396-408 (2016)
PMID: 26975655

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-118672 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
site-specific DNA-methyltransferase (adenine-specific) Chains: A, B
Molecule details ›
Chains: A, B
Length: 1406 amino acids
Theoretical weight: 160.72 KDa
Source organism: Lactococcus lactis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93R01 (Residues: 166-1570; Coverage: 90%)
Sequence domains:
DNA (5'-D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 23 nucleotides
Theoretical weight: 6.93 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 23 nucleotides
Theoretical weight: 7.18 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 87.4Å b: 222.29Å c: 117.41Å
α: 90° β: 105.14° γ: 90°
R-values:
R R work R free
0.231 0.229 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

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

2 mentions without citation

Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.
Kulkarni et al. (2016)
1 more