› 2nyt

X-ray diffraction
2.5Å resolution

The APOBEC2 Crystal Structure and Functional Implications for AID

Released:
DOI: 10.2210/pdb2nyt/pdb
PDB entry 2nyt coloured by chain, front view.
PDB entry 2nyt coloured by chain, side view.
PDB entry 2nyt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The APOBEC-2 crystal structure and functional implications for the deaminase AID.
Prochnow C, Bransteitter R, Klein MG, Goodman MF, Chen XS
Nature 445 447-51 (2007)
PMID: 17187054

Function and Biology Details

Reaction catalysed: 
Cytosine(6666) in apolipoprotein B mRNA + H(2)O = uracil(6666) in apolipoprotein B mRNA + NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195092 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C->U-editing enzyme APOBEC-2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 190 amino acids
Theoretical weight: 21.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y235 (Residues: 41-224; Coverage: 82%)
Gene name: APOBEC2
Sequence domains: APOBEC-like C-terminal domain
Structure domains: Cytidine Deaminase, domain 2

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1, null
Spacegroup: P212121
Unit cell:
a: 37.841Å b: 89.41Å c: 245.77Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.246 0.295
Expression system: Escherichia coli

Quick links

Citations

33 review citations

The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements.
Chiu et al. (2008)
32 more

32 mentions without citation

The AID/APOBEC family of nucleic acid mutators.
Conticello SG. (2008)
31 more