› 5tpr

X-ray diffraction
1.7Å resolution

Desmethyl-4-deoxygadusol synthase from Anabaena variabilis (Ava_3858) with NAD+ and Zn2+ bound

Released:
DOI: 10.2210/pdb5tpr/pdb
PDB entry 5tpr coloured by chain, front view.
PDB entry 5tpr coloured by chain, side view.
PDB entry 5tpr coloured by chain, top view.
Source organism: Trichormus variabilis ATCC 29413
Primary publication:
Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes.
Osborn AR, Kean KM, Alseud KM, Almabruk KH, Asamizu S, Lee JA, Karplus PA, Mahmud T
ACS Chem Biol 12 979-988 (2017)
PMID: 28182402

Function and Biology Details

Reaction catalysed: 
D-sedoheptulose 7-phosphate = demethyl-4-deoxygadusol + phosphate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174750 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Demethyl-4-deoxygadusol synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 444 amino acids
Theoretical weight: 50.13 KDa
Source organism: Trichormus variabilis ATCC 29413
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3M6C3 (Residues: 1-410; Coverage: 100%)
Gene name: Ava_3858
Sequence domains: 3-dehydroquinate synthase
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
4 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 6 x SO4
Ligand PEG 2 x PEG
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P212121
Unit cell:
a: 66.5Å b: 120.261Å c: 133.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.156 0.183
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The Syntrophy hypothesis for the origin of eukaryotes revisited.
López-García et al. (2020)
7 other articles

3 mentions without citation

The sedoheptulose 7-phosphate cyclases and their emerging roles in biology and ecology.
Osborn et al. (2017)
2 more