5HC7

Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with S-thiolo-isopentenyldiphosphate

Summary for 5HC7

• Entry DOI: 10.2210/pdb5hc7/pdb
• Related: 5HC6 5HC8
• Descriptor: prenyltransference for protein, MAGNESIUM ION, DIMETHYLALLYL S-THIOLODIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: substrate binding, transferase, lavandulyl, inhibitor, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Lavandula lanata
• Total number of polymer chains: 1
• Total formula weight: 30300.27

Authors

Liu, M.X.,Liu, W.D.,Gao, J.,Zheng, Y.Y.,Chen, C.C.,Guo, R.T. (deposition date: 2016-01-04, release date: 2016-03-02, Last modification date: 2023-11-08)

Primary citation

Liu, M.X.,Chen, C.C.,Chen, L.,Xiao, X.S.,Zheng, Y.Y.,Huang, J.W.,Liu, W.D.,Ko, T.P.,Cheng, Y.S.,Feng, X.X.,Oldfield, E.,Guo, R.T.,Ma, Y.H.
Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase
Angew.Chem.Int.Ed.Engl., 55:4721-4724, 2016

PubMed Abstract: We report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a precursor to the fragrance lavandulol. The structure is similar to that of the bacterial cis-prenyl synthase, undecaprenyl diphosphate synthase (UPPS), and contains an allylic site (S1) in which DMAPP ionizes and a second site (S2) which houses the DMAPP nucleophile. Both S-thiolo-dimethylallyl diphosphate and S-thiolo-isopentenyl diphosphate bind intact to S2, but are cleaved to (thio)diphosphate, in S1. His78 (Asn in UPPS) is essential for catalysis and is proposed to facilitate diphosphate release in S1, while the P1 phosphate in S2 abstracts a proton from the lavandulyl carbocation to form the LPP product. The results are of interest since they provide the first structure and structure-based mechanism of this unusual prenyl synthase.

PubMed: 26922900
DOI: 10.1002/anie.201600656

Experimental method

X-RAY DIFFRACTION (2.05 Å)