Advertisement

Extremophiles

, Volume 22, Issue 6, pp 877–888 | Cite as

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

  • Tatiana E. Petrova
  • Konstantin M. Boyko
  • Alena Yu. Nikolaeva
  • Tatiana N. Stekhanova
  • Eugeny V. Gruzdev
  • Andrey V. Mardanov
  • Viktor S. Stroilov
  • Jennifer A. Littlechild
  • Vladimir O. Popov
  • Ekaterina Yu. Bezsudnova
Original Paper
  • 100 Downloads

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.

Keywords

Prenyltransferase Biocatalysis Enzyme structure Archaea Structure activity relationship 

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

Notes

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

792_2018_1044_MOESM1_ESM.pdf (109 kb)
Supplementary material 1 (PDF 108 kb)

References

  1. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68:352–367CrossRefPubMedPubMedCentralGoogle Scholar
  2. Artz JD, Wernimont AK, Dunford JE, Schapira M, Dong A, Zhao Y, Lew J, Russell RG, Ebetino FH, Oppermann U, Hui R (2011) Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites. J Biol Chem 286:3315–3322CrossRefPubMedGoogle Scholar
  3. Battye GG, Kontogiannis L, Johnson O, Powell HR, Leslie AGW (2011) Acta Crystallogr Biol Crystallogr 67:271–281CrossRefGoogle Scholar
  4. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Chem 72:248–254Google Scholar
  5. Burke CC, Wildung MR, Croteau R (1999) Ceranyl diphosphate synthase: cloning, expression, and characterization of this prenyltransferase as a heterodimer. Proc Natl Acad Sci USA 96:13062–13067CrossRefPubMedGoogle Scholar
  6. Cao R, Chen CK, Guo RT, Wang AH, Oldfield E (2008) Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases. Proteins 73:431–439CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chang TH, Guo RT, Ko TP, Wang AH, Liag PH (2006) Crystal structure of type-III geranylgeranyl pyrophosphate synthase from Saccharomyces cerevisiae and the mechanism of product chain length determination. J Biol Chem 281:14991–15000CrossRefPubMedGoogle Scholar
  8. Chen A, Poulter CD (1993) Purification and characterization of farnesyl diphosphate/geranylgeranyldiphosphate synthase. A thermostable bifunctional enzyme from Methanobacterium thermoautotrophicum. J Biol Chem 268:11002–11007PubMedGoogle Scholar
  9. Chen CKM, Hudock MP, Zhang Y, Guo RT, Cao R, No JH, Liang PH, Ko TP, Chang TH, Chang SC, Song Y, Axelson J, Kumar A, Wang AH, Oldfield E (2008) Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation. J Med Chem 51:5594–5607CrossRefPubMedCentralGoogle Scholar
  10. Diederichs K, Karplus PA (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4:269–275CrossRefPubMedGoogle Scholar
  11. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132CrossRefPubMedGoogle Scholar
  12. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr Biol Crystallogr 62:72–82CrossRefGoogle Scholar
  13. Fujiwara S, Yamanaka A, Hirooka K, Kobayashi A, Imanaka T, Fukusaki E (2004) Temperature-dependent modulation of farnesyl diphosphate/geranylgeranyl diphosphate synthase from hyperthermophilic archaea. Biochem Biophys Res Commun 325:1066–1074CrossRefPubMedGoogle Scholar
  14. Gabelli SB, McLellan JS, Montalvetti A, Oldfield E, Docampo R, Amzel LM (2006) Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: implications for drug design. Proteins 621:80–88Google Scholar
  15. Guo RT, Kuo CJ, Chou CC, Ko TP, Shr HL, Liang PH, Wanq AH (2004a) Crystal Structure of octaprenyl pyrophosphate synthase from hyperthermophilic Thermotoga maritima and mechanism of product chain length determination. J Biol Chem 279:4903–4912CrossRefPubMedGoogle Scholar
  16. Guo RT, Kuo CJ, Ko TP, Chou CC, Liang PH, Wang AHJ (2004b) A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produced unprecedented long chain trans-prenyl products. Biochemistry 43:7678–7686CrossRefPubMedGoogle Scholar
  17. Guo RT, Cao R, Liang PH, Ko TP, Chang TH, Hudock MP, Jeng WY, Chen CK, Zhang Y, Song Y, Kuo CJ, Yin F, Oldfield E, Wang AH (2007) Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases. Proc Natl Acad Sci USA 104:10022–10027CrossRefPubMedGoogle Scholar
  18. Han X, Chen CC, Kuo CJ, Huang CH, Zheng Y, Ko TP, Zhu Z, Feng X, Wang K, Oldfield E, Wang AH, Liang PH, Guo RT, Ma Y (2015) Crystal Structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms. Proteins 83:37–45CrossRefPubMedGoogle Scholar
  19. Hemmi H, Ikejiri S, Yamashita S, Nishino T (2002) Novel medium-chain prenyldiphosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. J Bacteriol 184:615–620CrossRefPubMedPubMedCentralGoogle Scholar
  20. Hemmi H, Noike M, Nakayama T, Nishino T (2003) An alternative mechanism of product chain-length determination in type III geranylgeranyl diphosphate synthase. Eur J Biochem 270:2186–2194CrossRefPubMedGoogle Scholar
  21. Hosfield DJ, Zhang Y, Dougan DR, Broun A, Tari LW, Swanson RV, Finn J (2004) Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis. J Biol Chem 279:8526–8529CrossRefPubMedGoogle Scholar
  22. Jain S, Caforio A, Driessen AJM (2014) Biosynthesis of archaeal membrane ether lipids. Front Microbiol 5:641CrossRefPubMedPubMedCentralGoogle Scholar
  23. Jordão FM, Gabriel HB, Alves JM, Angeli CB, Bifano TD, Breda A, de Azevedo MF, Basso LA, Wunderlich G, Kimura EA, Katzin AM (2013) Cloning and characterization of bifunctional enzyme farnesyl diphosphate/geranylgeranyl diphosphate synthase from Plasmodium falciparum. Malar J 12:184CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kavanagh KL, Dunford JE, Bunkoczi G, Russell RG, Oppermann U (2006) The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding. J Biol Chem 281:22004–22012CrossRefPubMedGoogle Scholar
  25. Kellogg BA, Poulter CD (1997) Chain elongation in the isoprenoid biosynthetic pathway. Curr Opin Chem Biol 1:570–578CrossRefPubMedGoogle Scholar
  26. Kloer DP, Welsch R, Beyer P, Schulz GE (2006) Structure and reaction geometry of geranylgeranyl diphosphate synthase from sinapis alba. Biochemistry 45:15197–15204CrossRefPubMedGoogle Scholar
  27. Koga Y, Morii H (2007) Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev 71:97–120CrossRefPubMedPubMedCentralGoogle Scholar
  28. Krissinel E, Henrick K (2007) Interference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797CrossRefPubMedGoogle Scholar
  29. Kuzuguchi T, Morita Y, Sagami I, Sagami H, Ogura K (1999) Human geranylgeranyl diphosphate synthase. cDNA cloning and expression. J Biol Chem 274:5888–5894CrossRefPubMedGoogle Scholar
  30. Lai D, Lluncor B, Schröder I, Gunsalus RP, Liao JC, Monbouquette HG (2009) Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglycerylphosphate. Metab Eng 11:184–191CrossRefPubMedPubMedCentralGoogle Scholar
  31. Li ZH, Cintrón R, Koon NA, Moreno SNJ (2012) The N-terminus and the chain-length determination (CLD) domain play a role in the length of the isoprenoid product of the bifunctional Toxoplasma gondii farnesyl-diphosphate synthase. Biochemistry 51:7533–7540CrossRefPubMedPubMedCentralGoogle Scholar
  32. Liang PH (2009) Reaction kinetics, catalytic mechanisms, conformational changes, and inhibitor design for prenyltransferases. Biochemistry 48:6562–6570CrossRefPubMedGoogle Scholar
  33. Ling Y, Li ZH, Miranda K, Oldfield E, Moreno SN (2007) The farnesyl-diphosphate/geranylgeranyl-diphosphate synthase of Toxoplasma gondii is a bifunctional enzyme and a molecular target of bisphosphonates. J Biol Chem 282:30804–30816CrossRefPubMedGoogle Scholar
  34. Long F, Vagin A, Young P, Murshudov GN (2006) BALBES: a molecular replacement pipeline. Acta Crystallogr Biol Crystallogr 64:125–132CrossRefGoogle Scholar
  35. Mann M, Thomas JA, Peters RJ (2011) Rv0989c encodes a novel (E)-geranyl diphosphate synthase facilitating decaprenyl diphosphate biosynthesis in Mycobacterium tuberculosis. FEBS Lett 585:549–554CrossRefPubMedPubMedCentralGoogle Scholar
  36. Mao J, Mukherjee S, Zhang Y, Cao R, Sanders JM, Song Y, Zhang Y, Meints GA, Gao YG, Mukkamala D, Hudock MP, Oldfield E (2006) Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase–bisphosphonate complexes. J Am Chem Soc 128:14485–14497CrossRefPubMedGoogle Scholar
  37. Mardanov AV, Slododkina GB, Slobodkin AI, Beletsky AV, Gavrilov SN, Kublanov IV, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV (2015) The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon. Appl Environ Microbiol 81:1003–1012CrossRefPubMedPubMedCentralGoogle Scholar
  38. Noike M, Katagiri T, Nakayama T, Koyama T, Nishino T, Hemmi H (2008) The product chain length determination mechanism of type II geranylgeranyl diphosphate synthase requires subunit interaction. FEBS J 275:3921–3933CrossRefPubMedGoogle Scholar
  39. Ogawa T, Yoshimura T, Hemmi H (2010) Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: different role, different evolution. Biochem Biophys Res Commun 393:16–20CrossRefPubMedGoogle Scholar
  40. Ogura K, Koyama T (1998) Enzymatic aspects of isoprenoid chain elongation. Chem Rev 98:1263–1276CrossRefPubMedGoogle Scholar
  41. Ohnuma S, Suzuki M, Nishino T (1994) Archaebacterial ether-linked lipid biosynthetic gene. Expression cloning, sequencing, and characterization of geranylgeranyl-diphosphate synthase. J Biol Chem 269:14792–14797PubMedGoogle Scholar
  42. Ohnuma S, Hirooka K, Hemmi H, Ishida C, Ohto C, Nishino T (1996a) Conversion of product specificity of archaebacterial geranylgeranyl-diphosphate synthase. Identification of essential amino acid residues for chain length determination of prenyltransferase reaction. J Biol Chem 271:18831–18837CrossRefPubMedGoogle Scholar
  43. Ohnuma SI, Nakazawa T, Hemmi H, Hallberg AM, Koyama T, Ogura K, Nishino T (1996b) Conversion from farnesyl diphosphate synthase to geranylgeranyl diphosphate synthase by random chemical mutagenesis. J Biol Chem 271:10087–10095CrossRefPubMedGoogle Scholar
  44. Ohnuma S, Hirooka K, Ohto C, Nishino T (1997) Conversion from archaeal geranylgeranyl diphosphate synthase to farnesyl diphosphate synthase. Two amino acids before the first aspartate-rich motif solely determine eukaryotic farnesyl diphosphate synthase activity. J Biol Chem 272:5192–5198CrossRefPubMedGoogle Scholar
  45. Ohnuma SI, Hirooka K, Tsuruoka N, Yano M, Ohto C, Nakane H, Nishino T (1998) A pathway where polyprenyl diphosphate elongates in prenyltransferase. Insight into a common mechanism of chain length determination of prenyltransferases. J Biol Chem 273:26705–26713CrossRefPubMedGoogle Scholar
  46. Padilla JE, Yeates TO (2003) A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr Biol Crystallogr 59:1124–1130CrossRefGoogle Scholar
  47. Park J, Lin YS, De Schutter JW, Tsantrizos YS, Berghuis AM (2012) Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme’s active site closure. BMC Struct Biol 12:32CrossRefPubMedPubMedCentralGoogle Scholar
  48. Park J, Zielinski M, Magder A, Tsantrizos YS, Berghuis AM (2017) Human farnesyl pyrophosphate synthase is allosterically inhibited by its own product. Nat Commun 8:14132CrossRefPubMedPubMedCentralGoogle Scholar
  49. Rondeau JM, Bitsch F, Bourgier E, Geiser M, Hemmig R, Kroemer M (2006) Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs. Chem Med Chem 1:267–273CrossRefPubMedGoogle Scholar
  50. Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Miki K (2011) Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. J Biol Chem 286:3729–3740CrossRefPubMedGoogle Scholar
  51. Schmidberger JW, Schnell R, Schneider G (2015) Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa. Acta Crystallogr Biol Crystallogr 72:721–731CrossRefGoogle Scholar
  52. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539CrossRefPubMedPubMedCentralGoogle Scholar
  53. Slobodkina GB, Kolganova TV, Querellou J, Bonch-Osmolovskaya EA, Slobodkin AI (2009) Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 59:2880–2883CrossRefPubMedGoogle Scholar
  54. Tachibana A, Yano Y, Otani S, Nomura N, Sako Y, Taniguchi M (2000) Novel prenyltransferase gene encoding farnesylgeranyldiphosphate synthase from a hyperthermophilic archaeon Aeropyrum pernix. Molecular evolution with alteration in product specificity. Eur J Biochem 267:321–328CrossRefPubMedGoogle Scholar
  55. Tarshis LC, Proteau PJ, Kellogg BA, Sacchettini JC, Poulter CD (1996) Regulation of product chain length by isoprenyl diphosphate synthases. Proc Natl Acad Sci USA 93:15018–15023CrossRefPubMedGoogle Scholar
  56. Villanueva L (2014) A re-evaluation of the archaeal membrane lipid biosynthetic pathway. Nat Rev Microbiol 12:438–448CrossRefPubMedGoogle Scholar
  57. Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD (2013) Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci USA 110:1196–1202CrossRefGoogle Scholar
  58. Wang G, Dixon RA (2009) Heterodimeric geranyl(geranyl)diphosphate synthase from hop (Humulus lupulus) and the evolution of monoterpene biosynthesis. Proc Natl Acad Sci USA 106:9914–9919CrossRefPubMedGoogle Scholar
  59. Wang K, Ohnuma S (1999) Chain-length determination mechanism of isoprenyl diphosphate synthases and implications for molecular evolution. Trends Biochem Sci 24:445–451CrossRefPubMedGoogle Scholar
  60. Winkelblech J, Fan A, Li SM (2015) Prenyltransferases as key enzymes in primary and secondary metabolism. Appl Microbiol Biotechnol 99:7379–7397CrossRefPubMedGoogle Scholar
  61. Zhang YW, Li XY, Koyama T (2000) Chain length determination of prenyltransferases: both heteromeric subunits of medium-chain (E)-prenyl diphosphate synthase are involved in the product chain length determination. Biochemistry 39:12717–12722CrossRefPubMedGoogle Scholar

Copyright information

© Springer Japan KK, part of Springer Nature 2018

Authors and Affiliations

  • Tatiana E. Petrova
    • 1
  • Konstantin M. Boyko
    • 2
    • 3
  • Alena Yu. Nikolaeva
    • 2
  • Tatiana N. Stekhanova
    • 2
  • Eugeny V. Gruzdev
    • 2
  • Andrey V. Mardanov
    • 2
  • Viktor S. Stroilov
    • 4
  • Jennifer A. Littlechild
    • 5
  • Vladimir O. Popov
    • 2
    • 3
  • Ekaterina Yu. Bezsudnova
    • 2
  1. 1.Institute of Mathematical Problems of Biology, RAS, Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of SciencesPushchinoRussian Federation
  2. 2.Research Center of Biotechnology of the Russian Academy of SciencesMoscowRussian Federation
  3. 3.NBICS Center, National Research Centre “Kurchatov Institute”MoscowRussian Federation
  4. 4.N. D. Zelinsky Institute of Organic Chemistry (ZIOC RAS)MoscowRussian Federation
  5. 5.Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK

Personalised recommendations