OpenLB
Open Library of Bioscience
Advanced Search
Open biology
01, 2023;13 (1): 220287.

Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase.

Wenbo Li, Georgina C Girt, Ashish Radadiya, James J P Stewart, Nigel G J Richards, James H Naismith
Author Information
  1. Wenbo Li: Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK.
  2. Georgina C Girt: Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK. ORCID
  3. Ashish Radadiya: School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK. ORCID
  4. James J P Stewart: Stewart Computational Chemistry, Colorado Springs, CO 80921, USA.
  5. Nigel G J Richards: School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK. ORCID
  6. James H Naismith: Structural Biology, The Rosalind Franklin Institute, Didcot OX11 0QS, UK. ORCID
PMID: 36629016 DOI: 10.1098/rsob.220287

Abstract

The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1-pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.

Keywords

C-nucleoside X-ray crystallography biosynthesis formycin

References

  1. Biotechnol Adv. 2021 Jan-Feb;46:107673 [PMID: 33276073]
  2. J Biol Chem. 1979 Sep 25;254(18):8819-24 [PMID: 479162]
  3. Biochemistry. 1997 Sep 16;36(37):11061-8 [PMID: 9333323]
  4. Nat Commun. 2021 Dec 10;12(1):7205 [PMID: 34893622]
  5. Appl Environ Microbiol. 2020 Jan 7;86(2): [PMID: 31676476]
  6. Microbiol Resour Announc. 2020 Apr 2;9(14): [PMID: 32241862]
  7. Antiviral Res. 2017 Jun;142:63-67 [PMID: 28336346]
  8. Angew Chem Int Ed Engl. 2017 Jun 26;56(27):7920-7923 [PMID: 28558156]
  9. Beilstein J Org Chem. 2018 Apr 5;14:772-785 [PMID: 29719574]
  10. ChemMedChem. 2021 May 6;16(9):1403-1419 [PMID: 33427377]
  11. Angew Chem Int Ed Engl. 2019 Nov 11;58(46):16512-16516 [PMID: 31518483]
  12. Org Biomol Chem. 2014 Nov 14;12(42):8367-78 [PMID: 25181003]
  13. J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):335-343 [PMID: 30465105]
  14. iScience. 2019 Dec 20;22:430-440 [PMID: 31816530]
  15. Chem Rev. 2009 Dec;109(12):6729-64 [PMID: 19761208]
  16. J Med Chem. 2016 Mar 24;59(6):2301-11 [PMID: 26513594]
  17. Structure. 2000 Dec 15;8(12):1309-18 [PMID: 11188695]
  18. Science. 2020 Aug 7;369(6504):725-730 [PMID: 32764073]
  19. J Med Chem. 2018 Mar 22;61(6):2211-2226 [PMID: 28792763]
  20. Org Lett. 2020 Dec 4;22(23):9287-9291 [PMID: 33210930]
  21. Bioorg Med Chem. 2009 Jan 15;17(2):794-803 [PMID: 19095456]
  22. J Med Chem. 2016 Dec 8;59(23):10343-10382 [PMID: 27607900]
  23. Cell Chem Biol. 2019 Apr 18;26(4):493-501.e5 [PMID: 30713097]
  24. Molecules. 2021 Jan 19;26(2): [PMID: 33478059]
  25. Microb Cell Fact. 2022 Jan 4;21(1):2 [PMID: 34983520]
  26. Cell Chem Biol. 2018 May 17;25(5):540-549.e4 [PMID: 29551347]
  27. J Org Chem. 2021 Dec 3;86(23):16625-16640 [PMID: 34756029]
  28. J Am Chem Soc. 2019 Apr 17;141(15):6127-6131 [PMID: 30942582]
  29. Chembiochem. 2020 Mar 2;21(5):644-649 [PMID: 31482654]
  30. Org Lett. 2017 Mar 17;19(6):1426-1429 [PMID: 28233490]
  31. Structure. 2000 Dec 15;8(12):1247-57 [PMID: 11188689]
  32. Nature. 2016 Mar 17;531(7594):381-5 [PMID: 26934220]
  33. Biochemistry. 2012 Nov 13;51(45):9245-55 [PMID: 23066817]
  34. Biochemistry. 2002 Oct 8;41(40):11990-6 [PMID: 12356299]
  35. Chem Rev. 2014 Sep 24;114(18):9154-218 [PMID: 25144792]
  36. Open Biol. 2023 Jan;13(1):220287 [PMID: 36629016]
  37. Angew Chem Int Ed Engl. 2021 Jul 26;60(31):17148-17154 [PMID: 34048627]
  38. ACS Chem Biol. 2017 Jun 16;12(6):1472-1477 [PMID: 28418235]
  39. J Mol Model. 2013 Jan;19(1):1-32 [PMID: 23187683]
  40. Org Process Res Dev. 2020 Aug 05;24(9):1772-1777 [PMID: 37556261]
  41. Chem Commun (Camb). 2020 Jul 14;56(55):7617-7620 [PMID: 32515440]
  42. Nature. 2020 Sep;585(7824):273-276 [PMID: 32516797]
  43. Chem Soc Rev. 2021 Feb 15;50(3):1968-2009 [PMID: 33325938]

MeSH Term

Nucleosides
Catalysis
Crystallography, X-Ray

Chemicals

Nucleosides
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 9

Word Cloud

Created with Highcharts 10.0.0ForTformationC-CbondC-nucleosideacidformycinchemicalbiosyntheticenzymecatalyses4-amino-1-pyrazoledicarboxylicMgPRPPproduceprecursortransformationcatalysedinterestoneexamplestakesplaceviaelectrophilicsubstitutionsmallaromaticheterocycleadditioncapablediscriminatingaminopyrazoledicarboxylicanalogueaminereplacedhydroxylgroupremarkablefeatgivenstericelectronicsimilaritiestwomoleculesreportbiophysicalmeasurementsstructuralbiologyquantumcalculationsprovidedetailedmolecularpictureForT-catalysedconformationalchangescoupledcatalysisfindingssetsceneemployingengineeredvariantsbiocatalyticproductionnovelanti-viralC-nucleotideanaloguesExperimentalcomputationalsnapshotssynthaseX-raycrystallographybiosynthesis

Similar Articles

Cited By