› 5jj4

X-ray diffraction
2.81Å resolution

Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein

Released:
DOI: 10.2210/pdb5jj4/pdb
PDB entry 5jj4 coloured by chain, front view.
PDB entry 5jj4 coloured by chain, side view.
PDB entry 5jj4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.
Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF
DNA Repair (Amst) 43 48-56 (2016)
PMID: 27258794

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142660 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Maltose/maltodextrin-binding periplasmic protein; Single-stranded DNA cytosine deaminase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 546 amino acids
Theoretical weight: 61.46 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEY0 (Residues: 27-393; Coverage: 99%)
  • Canonical: Q9GZX7 (Residues: 23-183; Coverage: 81%)
Gene names: AICDA, AID, ECs5017, Z5632, malE
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
2 bound ligands:
Ligand ZN 3 x ZN
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 106.793Å b: 96.806Å c: 108.692Å
α: 90° β: 102.86° γ: 90°
R-values:
R R work R free
0.185 0.183 0.232
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Progesterone-Related Immune Modulation of Pregnancy and Labor.
Shah et al. (2019)
7 more

7 mentions without citation

A Novel Regulator of Activation-Induced Cytidine Deaminase/APOBECs in Immunity and Cancer: Schrödinger's CATalytic Pocket.
King et al. (2017)
6 more