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Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans

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Abstract

A novel type 1 geranylgeranyl pyrophosphate synthase GACE1337 has been identified within the genome of a newly identified hyperthermophilic archaeon Geoglobus acetivorans. The enzyme has been cloned and over-expressed in Escherichia coli. The recombinant enzyme has been biochemically and structurally characterized. It is able to catalyze the synthesis of geranylgeranyl pyrophosphate as a major product and of farnesyl pyrophosphate in smaller amounts, as measured by gas chromatography–mass spectrometry at an elevated temperature of 60 °C. Its ability to produce two products is consistent with the fact that GACE1337 is the only short-chain isoprenyl diphosphate synthase in G. acetivorans. Attempts to crystallize the enzyme were successful only at 37 °C. The three-dimensional structure of GACE1337 was determined by X-ray diffraction to 2.5 Å resolution. A comparison of its structure with those of related enzymes revealed that the Geoglobus enzyme has the features of both type I and type III geranylgeranyl pyrophosphate synthases, which allow it to regulate the product length. The active enzyme is a dimer and has three aromatic amino acids, two Phe, and a Tyr, located in the hydrophobic cleft between the two subunits. It is proposed that these bulky residues play a major role in the synthetic reaction by controlling the product elongation.

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Abbreviations

IDS:

Isoprenyl diphosphate synthase

IPP:

Isopentenyl pyrophosphate

DMAPP:

Dimethylallyl pyrophosphate

GPP:

Geranyl pyrophosphate

FPP:

Farnesyl pyrophosphate

GGPP:

Geranylgeranyl pyrophosphate

FARM:

The first aspartate-rich motif

GFPP:

Geranylfarnesyl pyrophosphate

GACE1337:

Geranylgeranyl pyrophosphate synthase from archaeon G. acetivorans

GC-MS:

Gas chromatography–mass spectrometry

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Acknowledgements

This work was supported in part by the Russian Science Foundation Project 14-24-00172 (purification and structure determination), the Russian Foundation for Basic Research 16-04-01037a (structure refinement and analysis), the ERA-IB project THERMOGENE (cloning and expression) funded through the ERA-NET Scheme of the seventh EU Framework Programme by the Russian Foundation for Assistance to Small Innovative Enterprises, and by the Russian Federal Space Agency (crystallization and subsequent X-ray diffraction experiments). JAL acknowledges the THERMOGENE project and funding from the BBSRC, UK BB/L002035/1.

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Authors and Affiliations

  1. Institute of Mathematical Problems of Biology, RAS, Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Professor Vitkevich St., Pushchino, 142290, Russian Federation

    Tatiana E. Petrova

  2. Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow, 119071, Russian Federation

    Konstantin M. Boyko, Alena Yu. Nikolaeva, Tatiana N. Stekhanova, Eugeny V. Gruzdev, Andrey V. Mardanov, Vladimir O. Popov & Ekaterina Yu. Bezsudnova

  3. NBICS Center, National Research Centre “Kurchatov Institute”, Akad. Kurchatova sqr, 1, Moscow, 123182, Russian Federation

    Konstantin M. Boyko & Vladimir O. Popov

  4. N. D. Zelinsky Institute of Organic Chemistry (ZIOC RAS), Leninsky Prospekt, 47, Moscow, 119991, Russian Federation

    Viktor S. Stroilov

  5. Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK

    Jennifer A. Littlechild

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  1. Tatiana E. Petrova
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  2. Konstantin M. Boyko
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Petrova, T.E., Boyko, K.M., Nikolaeva, A.Y. et al. Structural characterization of geranylgeranyl pyrophosphate synthase GACE1337 from the hyperthermophilic archaeon Geoglobus acetivorans. Extremophiles 22, 877–888 (2018). https://doi.org/10.1007/s00792-018-1044-5

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