Skip to content

Research at St Andrews

Catalytic and anticatalytic snapshots of a short-form ATP phosphoribosyltransferase

Research output: Contribution to journalArticlepeer-review

Author(s)

Magnus Stephen Alphey, Gemma Fisher, Ying Ge, Eoin Rory Gould, Teresa Filipa Guerreiro Machado, Huanting Liu, Gordon John Florence, James Henderson Naismith, Rafael G da Silva

School/Research organisations

Abstract

Allosteric modulation of catalysis is a common regulatory strategy of flux-controlling biosynthetic enzymes. The enzyme ATP phosphoribosyltransferase (ATPPRT) catalyzes the first reaction in histidine biosynthesis, the magnesium-dependent condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate N1-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate (PPi). ATPPRT is allosterically inhibited by the final product of the pathway, histidine. Hetero-octameric ATPPRT consists of four catalytic subunits (HisGS) and four regulatory subunits (HisZ) engaged in intricate catalytic regulation. HisZ enhances HisGS catalysis in the absence of histidine while mediating allosteric inhibition in its presence. Here we report HisGS structures for the apoenzyme and complexes with substrates (PRPP, PRPP-ATP, PRPP-ADP), product (PRATP), and inhibitor (AMP), along with ATPPRT holoenzyme structures in complexes with substrates (PRPP, PRPP-ATP, PRPP-ADP) and product (PRATP). These 10 crystal structures provide an atomic view of the catalytic cycle and allosteric activation of Psychrobacter arcticus ATPPRT. In both ternary complexes with PRPP-ATP, the adenine ring is found in an anticatalytic orientation, rotated 180° from the catalytic rotamer. Arg32 interacts with phosphate groups of ATP and PRPP, bringing the substrates in proximity for catalysis. The negative charge repulsion is further attenuated by a magnesium ion sandwiched between the α- and β-phosphate groups of both substrates. HisZ binding to form the hetero-octamer brings HisGS subunits closer together in a tighter dimer in the Michaelis complex, which poises Arg56 from the adjacent HisGS molecule for cross-subunit stabilization of the PPi leaving group at the transition state. The more electrostatically preorganized active site of the holoenzyme likely minimizes the reorganization energy required to accommodate the transition state. This provides a structural basis for allosteric activation in which chemistry is accelerated by facilitating leaving group departure.
Close

Details

Original languageEnglish
Pages (from-to)5601-5610
Number of pages10
JournalACS Catalysis
Volume8
Issue number6
Early online date11 May 2018
DOIs
Publication statusPublished - 1 Jun 2018

    Research areas

  • Allostery, ATP phosphoribosyltransferase, Catalytic activation, HisG, Histidine, Biosynthesis, HisZ, Psychrophilic

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Kinetics and structure of a cold-adapted hetero-octameric ATP phosphoribosyltransferase

    Stroek, R., Ge, Y., Talbot, P. D., Glok, M. K., Bernas, K. E., Thomson, C. M., Gould, E. R., Alphey, M. S., Liu, H., Florence, G. J., Naismith, J. H. & da Silva, R. G., 7 Feb 2017, In: Biochemistry. 56, 5, p. 793-803 11 p.

    Research output: Contribution to journalArticlepeer-review

  2. Mapping the structural path for allosteric inhibition of a short-form ATP phosphoribosyltransferase by histidine

    Thomson, C. M., Alphey, M. S., Fisher, G. & da Silva, R. G., 16 Jul 2019, In: Biochemistry. 58, 28, p. 3078-3086

    Research output: Contribution to journalArticlepeer-review

  3. Dissecting the mechanism of (R)-3-hydroxybutyrate dehydrogenase by kinetic isotope effects, protein crystallography, and computational chemistry

    G. Machado, T. F., Purg, M., McMahon, S., Read, B., Oehler, V., Åqvist, J., Gloster, T. & da Silva, R. G., 18 Dec 2020, In: ACS Catalysis. 10, 24, p. 15019–15032

    Research output: Contribution to journalArticlepeer-review

  4. Structure‐based design, synthesis and biological evaluation of bis‐tetrahydropyran furan acetogenin mimics targeting the trypanosomatid F1 component of ATP synthase

    Zacharova, M., Tulloch, L., Gould, E., Fraser, A., King, E., Menzies, S., Smith, T. K. & Florence, G. J., 1 Sep 2019, In: European Journal of Organic Chemistry. 2019, 31-32, p. 5434-5440 8 p.

    Research output: Contribution to journalArticlepeer-review

  5. An exceptionally potent inhibitor of human CD73

    Bowman, C. E., da Silva, R. G., Pham, A. & Young, S. W., 6 Aug 2019, In: Biochemistry. 58, 31, p. 3331-3334 4 p.

    Research output: Contribution to journalArticlepeer-review

Related by journal

  1. Achieving strong coherency for a composite electrode via one-pot method with enhanced electrochemical performance in reversible solid oxide cells

    Tian, Y., Wang, W., Liu, Y., Naden, A., Xu, M., Wu, S., Chi, B., Pu, J. & Irvine, J. T. S., 19 Mar 2021, In: ACS Catalysis. 11, 6, p. 3704-3714 11 p.

    Research output: Contribution to journalArticlepeer-review

  2. Ultrarapid cerium(III)–NHC catalysts for high molar mass cyclic polylactide

    Kerr, R. W. F., Ewing, P., Raman, S. K., Smith, A. D., Williams, C. K. & Arnold, P. L., 15 Jan 2021, In: ACS Catalysis. 11, p. 1563-1569

    Research output: Contribution to journalArticlepeer-review

  3. A Ce/Ru codoped SrFeO3−δ perovskite for a coke-resistant anode of a symmetrical solid oxide fuel cell

    Li, B., He, S., Li, J., Yue, X., Irvine, J. T. S., Xie, D., Ni, J. & Ni, C., 18 Dec 2020, In: ACS Catalysis. 10, 24, p. 14398-14409 12 p.

    Research output: Contribution to journalArticlepeer-review

  4. Dissecting the mechanism of (R)-3-hydroxybutyrate dehydrogenase by kinetic isotope effects, protein crystallography, and computational chemistry

    G. Machado, T. F., Purg, M., McMahon, S., Read, B., Oehler, V., Åqvist, J., Gloster, T. & da Silva, R. G., 18 Dec 2020, In: ACS Catalysis. 10, 24, p. 15019–15032

    Research output: Contribution to journalArticlepeer-review

  5. Selective room-temperature hydrogenation of amides to amines and alcohols catalyzed by a ruthenium pincer complex and mechanistic insight

    Kar, S., Rauch, M., Kumar, A., Leitus, G., Ben-David, Y. & Milstein, D., 21 Apr 2020, In: ACS Catalysis. 10, p. 5511-5515 5 p.

    Research output: Contribution to journalArticlepeer-review

ID: 253149051

Top