2J1P

Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP

Summary for 2J1P

• Entry DOI: 10.2210/pdb2j1p/pdb
• Related: 2J1O
• Descriptor: GERANYLGERANYL PYROPHOSPHATE SYNTHETASE, GERANYLGERANYL DIPHOSPHATE, S-1,2-PROPANEDIOL, ... (5 entities in total)
• Functional Keywords: transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis, isoprenyl transtransferase, isoprenoid diphosphate synthase, transit peptide, chloroplast, geranylgeranyl diphosphate
• Biological source: SINAPIS ALBA (WHITE MUSTARD)
• Cellular location: Plastid, chloroplast stroma (Probable): Q43133
• Total number of polymer chains: 2
• Total formula weight: 65028.30

Authors

Kloer, D.P.,Welsch, R.,Beyer, P.,Schulz, G.E. (deposition date: 2006-08-15, release date: 2007-01-02, Last modification date: 2025-04-09)

Primary citation

Kloer, D.P.,Welsch, R.,Beyer, P.,Schulz, G.E.
Structure and Reaction Geometry of Geranylgeranyl Diphosphate Synthase from Sinapis Alba.
Biochemistry, 45:15197-, 2006

PubMed Abstract: The crystal structure of the geranylgeranyl diphosphate synthase from Sinapis alba (mustard) has been solved in two crystal forms at 1.8 and 2.0 A resolutions. In one of these forms, the dimeric enzyme binds one molecule of the final product geranylgeranyl diphosphate in one subunit. The chainfold of the enzyme corresponds to that of other members of the farnesyl diphosphate synthase family. Whereas the binding modes of the two substrates dimethylallyl diphosphate and isopentenyl diphosphate at the allyl and isopentenyl sites, respectively, have been established with other members of the family, the complex structure presented reveals for the first time the binding mode of a reaction product at the isopentenyl site. The binding geometry of substrates and product in conjunction with the protein environment and the established chemistry of the reaction provide a clear picture of the reaction steps and atom displacements. Moreover, a comparison with a ligated homologous structure outlined an appreciable induced fit: helix alpha8 and its environment undergo a large conformational change when either the substrate dimethylallyl diphosphate or an analogue is bound to the allyl site; only a minor conformational change occurs when the other substrate isopentenyl diphosphate or the product is bound to the isopentenyl site.

PubMed: 17176041
DOI: 10.1021/BI061572K

Experimental method

X-RAY DIFFRACTION (1.8 Å)