Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding.

Item request has been placed! ×
Item request cannot be made. ×
loading   Processing Request
Read More Add to Saved list
  • Additional Information
    • Source:
      Publisher: eLife Sciences Publications, Ltd Country of Publication: England NLM ID: 101579614 Publication Model: Electronic Cited Medium: Internet ISSN: 2050-084X (Electronic) Linking ISSN: 2050084X NLM ISO Abbreviation: Elife Subsets: MEDLINE
    • Publication Information:
      Original Publication: Cambridge, UK : eLife Sciences Publications, Ltd., 2012-
    • Subject Terms:
      Ribonucleotide Reductases*/metabolism ; Ribonucleotide Reductases*/chemistry ; Adenosine Triphosphate*/metabolism ; Protein Binding*; Allosteric Regulation ; Anaerobiosis ; Deoxyadenine Nucleotides/metabolism ; Catalytic Domain ; Protein Conformation ; Substrate Specificity ; Protein Multimerization ; Models, Molecular
    • Abstract:
      A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri . The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.
      Competing Interests: OB, IB, IR, PH, LH, SE, DL, BS, DL No competing interests declared
      (© 2023, Bimai et al.)
    • References:
      Science. 2020 Apr 24;368(6489):424-427. (PMID: 32217749)
      J Biol Chem. 1994 Oct 21;269(42):26052-7. (PMID: 7929317)
      J Biol Chem. 2000 Jan 28;275(4):2463-71. (PMID: 10644700)
      Nat Methods. 2017 Mar;14(3):290-296. (PMID: 28165473)
      Structure. 2016 Jun 7;24(6):906-17. (PMID: 27133024)
      Acta Crystallogr D Struct Biol. 2017 Jun 1;73(Pt 6):469-477. (PMID: 28580908)
      J Biol Chem. 2001 Sep 7;276(36):33488-94. (PMID: 11427536)
      Structure. 2001 Aug;9(8):739-50. (PMID: 11587648)
      J Biol Chem. 2008 Dec 19;283(51):35310-8. (PMID: 18835811)
      FASEB J. 2018 Aug;32(8):4067-4069. (PMID: 30059250)
      Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. (PMID: 20383002)
      PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: 22039361)
      Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. (PMID: 31588918)
      Nucleic Acids Res. 2022 Jul 5;50(W1):W210-W215. (PMID: 35610055)
      Bioinformatics. 2021 Jul 27;37(13):1926-1927. (PMID: 33079991)
      Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21046-51. (PMID: 22160671)
      Mol Syst Biol. 2011 Oct 11;7:539. (PMID: 21988835)
      Science. 1999 Mar 5;283(5407):1499-504. (PMID: 10066165)
      J Biol Chem. 2004 Apr 9;279(15):14496-501. (PMID: 14752109)
      Proteins. 1994 Jul;19(3):183-98. (PMID: 7937733)
      Life (Basel). 2015 Feb 27;5(1):604-36. (PMID: 25734234)
      Anal Biochem. 1990 Aug 15;189(1):138-41. (PMID: 2278383)
      Protein Sci. 2022 Dec;31(12):e4483. (PMID: 36307939)
      J Am Chem Soc. 2022 Mar 23;144(11):5087-5098. (PMID: 35258967)
      Nat Commun. 2022 May 16;13(1):2700. (PMID: 35577776)
      J Mol Biol. 2003 Oct 31;333(4):721-45. (PMID: 14568533)
      Elife. 2018 Feb 01;7:. (PMID: 29388911)
      J Biol Chem. 2013 Mar 22;288(12):8198-8208. (PMID: 23372162)
      Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
      Elife. 2018 Feb 20;7:. (PMID: 29460780)
      Commun Biol. 2021 Jul 15;4(1):874. (PMID: 34267316)
      Protein Sci. 2021 Jan;30(1):70-82. (PMID: 32881101)
      J Biol Chem. 2006 Sep 1;281(35):25287-96. (PMID: 16829681)
      Nucleic Acids Res. 2019 Jul 2;47(W1):W414-W422. (PMID: 31114897)
      Anal Chem. 1996 Jun 1;68(11):1895-904. (PMID: 21619100)
      Chem Rev. 2022 Apr 27;122(8):7562-7623. (PMID: 34493042)
      J Biol Chem. 2000 Jun 30;275(26):19443-8. (PMID: 10748029)
      J Mol Microbiol Biotechnol. 2000 Apr;2(2):191-4. (PMID: 10939243)
      Elife. 2022 Sep 01;11:. (PMID: 36047668)
      Crit Rev Biochem Mol Biol. 2012 Jan-Feb;47(1):50-63. (PMID: 22050358)
      Nat Struct Mol Biol. 2011 Mar;18(3):316-22. (PMID: 21336276)
      Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):E3756-65. (PMID: 25157154)
      BMC Bioinformatics. 2014 Jan 13;15:7. (PMID: 24410852)
      Biochemistry. 2016 Jan 19;55(2):373-81. (PMID: 26727048)
      PLoS One. 2015 Jul 06;10(7):e0128199. (PMID: 26147435)
      IUCrJ. 2019 Sep 18;6(Pt 6):1054-1063. (PMID: 31709061)
      Nucleic Acids Res. 2022 Jan 7;50(D1):D543-D552. (PMID: 34723319)
      J Biol Chem. 2020 Nov 13;295(46):15576-15587. (PMID: 32883811)
      J Biol Chem. 2015 Jul 10;290(28):17339-48. (PMID: 25971975)
      Crit Rev Biochem Mol Biol. 2017 Dec;52(6):674-695. (PMID: 28901199)
      Ann Rheum Dis. 2023 May;82(5):621-629. (PMID: 36627170)
      Structure. 2016 Jun 7;24(6):843-4. (PMID: 27276424)
      Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8759-62. (PMID: 7568012)
      Annu Rev Anal Chem (Palo Alto Calif). 2015;8:127-48. (PMID: 26048552)
      J Biol Chem. 2018 Oct 12;293(41):15889-15900. (PMID: 30166338)
    • Grant Information:
      2019-01400 Vetenskapsrådet; 2016-04855 Vetenskapsrådet; CAN 20 1210 PjF Cancerfonden
    • Contributed Indexing:
      Keywords: ATP-cone; Prevotella copri; allosteric regulation; biochemistry; chemical biology; glycyl radical; ribonucleotide reductase
    • Accession Number:
      EC 1.17.4.- (Ribonucleotide Reductases)
      8L70Q75FXE (Adenosine Triphosphate)
      0 (Deoxyadenine Nucleotides)
      K8KCC8SH6N (2'-deoxyadenosine triphosphate)
    • Publication Date:
      Date Created: 20240705 Date Completed: 20240705 Latest Revision: 20240707
    • Publication Date:
      20240707
    • Accession Number:
      PMC11226230
    • Accession Number:
      10.7554/eLife.89292
    • Accession Number:
      38968292