› 5vhv

X-ray diffraction
1.8Å resolution

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog

Released:
DOI: 10.2210/pdb5vhv/pdb
PDB entry 5vhv coloured by chain, front view.
PDB entry 5vhv coloured by chain, side view.
PDB entry 5vhv coloured by chain, top view.
Source organisms:
Primary publication:
Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.
Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF
EMBO J 37 63-74 (2018)
PMID: 29054852

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111158 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA alkylation repair protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 361 amino acids
Theoretical weight: 40.54 KDa
Source organism: Pseudomonas fluorescens
Expression system: Escherichia coli
UniProt:
  • Canonical: C3K795 (Residues: 5-365; Coverage: 99%)
Gene name: PFLU_2162
Sequence domains: DNA alkylation repair enzyme
DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 11 nucleotides
Theoretical weight: 3.19 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 11 nucleotides
Theoretical weight: 3.38 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GOL 2 x GOL
Ligand MES 3 x MES
Ligand NA 2 x NA
Ligand 9B4 2 x 9B4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P61
Unit cell:
a: 198.373Å b: 198.373Å c: 60.189Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.142 0.141 0.164
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

The Similarities between Human Mitochondria and Bacteria in the Context of Structure, Genome, and Base Excision Repair System.
Boguszewska et al. (2020)
6 more

2 mentions without citation

Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.
Shi et al. (2018)
1 more