6LOO

Crystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate

Summary for 6LOO

• Entry DOI: 10.2210/pdb6loo/pdb
• Descriptor: Tetraprenyl-beta-curcumene synthase, phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate, phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate, ... (4 entities in total)
• Functional Keywords: terpene synthase, lyase
• Biological source: Bacillus alcalophilus ATCC 27647 = CGMCC 1.3604
• Total number of polymer chains: 2
• Total formula weight: 85116.71

Authors

Fujihashi, M.,Inagi, H.,Miki, K. (deposition date: 2020-01-07, release date: 2020-11-18, Last modification date: 2023-11-29)

Primary citation

Stepanova, R.,Inagi, H.,Sugawara, K.,Asada, K.,Nishi, T.,Ueda, D.,Yasuno, Y.,Shinada, T.,Miki, K.,Fujihashi, M.,Sato, T.
Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.
Acs Chem.Biol., 15:1517-1525, 2020

PubMed Abstract: Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C-C) prenyl-diphosphates as substrates and no amino acid sequence homology with known TS. Conversion of long prenyl-diphosphates such as heptaprenyl-diphosphate (C) is unusual and has never been reported for Class I and II enzymes. Therefore, the characterization of Class IB enzymes is crucial to understand the reaction mechanism of the extensive terpene synthesis. Here, we report the crystal structure bound with a substrate surrogate and biochemical analysis of a Class IB TS, using the enzyme from (BalTS). The structure analysis revealed that the diphosphate part of the substrate is located around the two characteristic Asp-rich motifs, and the hydrophobic tail is accommodated in a unique hydrophobic long tunnel, where the C prenyl-diphosphate, the longest substrate of BalTS, can be accepted. Biochemical analyses of BalTS showed that the enzymatic property, such as Mg dependency, is similar to those of Class I enzymes. In addition, a new cyclic terpene was identified from BalTS reaction products. Mutational analysis revealed that five of the six Asp residues in the Asp-rich motifs and two His residues are essential for the formation of the cyclic skeleton. These results provided a clue to consider the application of the unusual large terpene synthesis by Class IB enzymes.

PubMed: 32227910
DOI: 10.1021/acschembio.0c00145

Experimental method

X-RAY DIFFRACTION (1.99 Å)