› 2zrw

X-ray diffraction
2.4Å resolution

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with FMN and IPP.

Released:
DOI: 10.2210/pdb2zrw/pdb
PDB entry 2zrw coloured by chain, front view.
PDB entry 2zrw coloured by chain, side view.
PDB entry 2zrw coloured by chain, top view.
Source organism: Saccharolobus shibatae
Primary publication:
New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
Unno H, Yamashita S, Ikeda Y, Sekiguchi SY, Yoshida N, Yoshimura T, Kusunoki M, Nakayama T, Nishino T, Hemmi H
J Biol Chem 284 9160-7 (2009)
PMID: 19158086

Function and Biology Details

Reaction catalysed: 
Isopentenyl diphosphate = prenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158301 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate delta-isomerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 368 amino acids
Theoretical weight: 40.48 KDa
Source organism: Saccharolobus shibatae
Expression system: Escherichia coli
UniProt:
  • Canonical: P61615 (Residues: 1-368; Coverage: 100%)
Gene names: J5U23_00185, fni, idi
Sequence domains: FMN-dependent dehydrogenase
Structure domains: Aldolase class I

Ligands and Environments


Cofactor: Ligand FMN 4 x FMN
2 bound ligands:
Ligand IPR 4 x IPR
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P43212
Unit cell:
a: 100.444Å b: 100.444Å c: 333.914Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.219
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Mechanistic aspects of carotenoid biosynthesis.
Moise et al. (2014)
8 more

1 mention without citation

New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
Unno et al. (2009)