› 7uxd

X-ray diffraction
1.5Å resolution

Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine.

Released:
DOI: 10.2210/pdb7uxd/pdb
PDB entry 7uxd coloured by chain, front view.
PDB entry 7uxd coloured by chain, side view.
PDB entry 7uxd coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state.
Maiti A, Hedger AK, Myint W, Balachandran V, Watts JK, Schiffer CA, Matsuo H
Nat Commun 13 7117 (2022)
PMID: 36402773

Function and Biology Details

Reaction catalysed: 
Cytosine in single-stranded DNA + H(2)O = uracil in single-stranded DNA + NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122198 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA dC->dU-editing enzyme APOBEC-3G Chain: A
Molecule details ›
Chain: A
Length: 199 amino acids
Theoretical weight: 23.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HC16 (Residues: 191-384; Coverage: 51%)
Gene names: APOBEC3G, MDS019
Sequence domains: APOBEC-like C-terminal domain
DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.7 KDa
Source organism: synthetic construct
Expression system: synthetic construct

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand DDN 1 x DDN

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 47.489Å b: 47.121Å c: 52.042Å
α: 90° β: 103.18° γ: 90°
R-values:
R R work R free
0.174 0.172 0.194
Expression systems:
  • Escherichia coli
  • synthetic construct

Quick links

Citations

2 citation in other articles

Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.
Harjes et al. (2023)
1 more

1 mention without citation

Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state.
Maiti et al. (2022)