› 5dz2

X-ray diffraction
2.11Å resolution

Geosmin synthase from Streptomyces coelicolor N-terminal domain complexed with three Mg2+ ions and alendronic acid

Released:
DOI: 10.2210/pdb5dz2/pdb
PDB entry 5dz2 coloured by chain, front view.
PDB entry 5dz2 coloured by chain, side view.
PDB entry 5dz2 coloured by chain, top view.
Source organism: Streptomyces coelicolor A3(2)
Primary publication:
Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.
Harris GG, Lombardi PM, Pemberton TA, Matsui T, Weiss TM, Cole KE, Köksal M, Murphy FV, Vedula LS, Chou WK, Cane DE, Christianson DW
Biochemistry 54 7142-55 (2015)
PMID: 26598179

Function and Biology Details

Reactions catalysed: 
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H(2)O = (-)-geosmin + acetone
(2E,6E)-farnesyl diphosphate + H(2)O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
(2E,6E)-farnesyl diphosphate = (-)-germacrene D + diphosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194960 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Germacradienol/geosmin synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 338 amino acids
Theoretical weight: 38.27 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X839 (Residues: 1-338; Coverage: 47%)
Gene names: SC9B1.20, SCO6073, cyc2
Sequence domains: Terpene synthase family 2, C-terminal metal binding
Structure domains: Farnesyl Diphosphate Synthase

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand 212 2 x 212
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 67.213Å b: 67.213Å c: 345.388Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.207 0.25
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Structural and Chemical Biology of Terpenoid Cyclases.
Christianson DW. (2017)
4 more

8 mentions without citation

Assembly-Line Catalysis in Bifunctional Terpene Synthases.
Faylo et al. (2021)
7 more