› 5hmc

X-ray diffraction
2.2Å resolution

Crystal structure of S. sahachiroi AziG complexed with 5-methyl naphthoic acid

Released:
DOI: 10.2210/pdb5hmc/pdb
PDB entry 5hmc coloured by chain, front view.
PDB entry 5hmc coloured by chain, side view.
PDB entry 5hmc coloured by chain, top view.
Source organism: Streptomyces sahachiroi
Primary publication:
Polyketide Ring Expansion Mediated by a Thioesterase, Chain Elongation and Cyclization Domain, in Azinomycin Biosynthesis: Characterization of AziB and AziG.
Mori S, Simkhada D, Zhang H, Erb MS, Zhang Y, Williams H, Fedoseyenko D, Russell WK, Kim D, Fleer N, Ealick SE, Watanabe CM
Biochemistry 55 704-14 (2016)
PMID: 26731610

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110154 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thioesterase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 141 amino acids
Theoretical weight: 15.42 KDa
Source organism: Streptomyces sahachiroi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B4XYA6 (Residues: 1-133; Coverage: 100%)
Gene name: azi13
Sequence domains: Thioesterase superfamily
Structure domains: Hotdog Thioesterase

Ligands and Environments

2 bound ligands:
Ligand 5NE 1 x 5NE
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: I4122
Unit cell:
a: 67.771Å b: 67.771Å c: 140.278Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.219
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Biosynthesis of DNA-Alkylating Antitumor Natural Products.
Nie et al. (2022)
1 other article

470 mentions without citation

TET enzymes, TDG and the dynamics of DNA demethylation.
Kohli et al. (2013)
469 more