Structure of the ForT/PRPP complex uncovers the mechanism of C-C bond formation in C-nucleotide antibiotic biosynthesis

C-C bond formation is at the heart of anabolism and organic chemistry, but relatively few enzymatic strategies for catalyzing this reaction are known. The enzyme ForT catalyzes C-C bond formation between 5’-phosphoribosyl-1’-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of the C-nucleotide formycin A 5’-phosphate; we now report the 2.5 Å resolution structure of the ForT/PRPP complex and thus locate the active site. Site-directed mutagenesis has identified those residues critical for PRPP recognition and catalysis. Structural conservation with GHMP kinases suggests that stabilization of the negatively charged pyrophosphate leaving group is crucial for catalysis in ForT. A mechanism for this new class of C-C bond forming enzymes is proposed. Entry for the Table of Contents A new class of enzymes catalyse C-C bond formation by irreversible CO2 and pyrophosphate production.

[1]  H. Feldmann,et al.  Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection , 2020, Proceedings of the National Academy of Sciences.

[2]  J. Lian,et al.  The Biosynthetic Gene Cluster of Pyrazomycin—A C‐Nucleoside Antibiotic with a Rare Pyrazole Moiety , 2020, Chembiochem : a European journal of chemical biology.

[3]  V. de Crécy-Lagard,et al.  PMP–diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c9cc06975e , 2019, Chemical communications.

[4]  Hung‐wen Liu,et al.  Identification of the C-Glycoside Synthases during Biosynthesis of the Pyrazole-C-Nucleosides Formycin and Pyrazofurin. , 2019, Angewandte Chemie.

[5]  T. Kuzuyama,et al.  Recent advances in the biosynthesis of nucleoside antibiotics , 2019, The Journal of Antibiotics.

[6]  Hung‐wen Liu,et al.  Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis. , 2019, Journal of the American Chemical Society.

[7]  Y. Kung,et al.  Structural insight into substrate and product binding in an archaeal mevalonate kinase , 2018, PloS one.

[8]  J. Naismith,et al.  Catalytic and Anticatalytic Snapshots of a Short-Form ATP Phosphoribosyltransferase , 2018 .

[9]  N. Richards,et al.  Second-Shell Hydrogen Bond Impacts Transition-State Structure in Bacillus subtilis Oxalate Decarboxylase. , 2018, Biochemistry.

[10]  Kartik W Temburnikar,et al.  Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides , 2018, Beilstein journal of organic chemistry.

[11]  F. Raushel,et al.  A combined experimental-theoretical study of the ligW-catalyzed decarboxylation of 5-carboxyvanillate in the metabolic pathway for lignin degradation , 2017 .

[12]  E. Clercq C-Nucleosides To Be Revisited. , 2016 .

[13]  William A. Lee,et al.  Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys , 2016, Nature.

[14]  E. De Clercq C-Nucleosides To Be Revisited. , 2016, Journal of medicinal chemistry.

[15]  P. Pawelek,et al.  The C-glycosyltransferase IroB from pathogenic Escherichia coli: identification of residues required for efficient catalysis. , 2014, Biochimica et biophysica acta.

[16]  G. Schneider,et al.  Structural basis for C-ribosylation in the alnumycin A biosynthetic pathway , 2013, Proceedings of the National Academy of Sciences.

[17]  N. Richards,et al.  Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases. , 2011, Analytical biochemistry.

[18]  Robert H. White The conversion of a phenol to an aniline occurs in the biochemical formation of the 1-(4-aminophenyl)-1-deoxy-D-ribitol moiety in methanopterin. , 2011, Biochemistry.

[19]  Michal Hocek,et al.  C-nucleosides: synthetic strategies and biological applications. , 2009, Chemical reviews.

[20]  Lester G. Carter,et al.  AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis , 2009, Nature chemical biology.

[21]  Narayanan Eswar,et al.  Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.

[22]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[23]  A. Ferré-D’Amaré,et al.  Pseudouridine synthases. , 2006, Chemistry & biology.

[24]  Mechanism of 4-(β-D-Ribofuranosyl)aminobenzene 5′-Phosphate Synthase, a Key Enzyme in the Methanopterin Biosynthetic Pathway* , 2004, Journal of Biological Chemistry.

[25]  A. Osterman,et al.  Structural basis for the catalysis and substrate specificity of homoserine kinase. , 2001, Biochemistry.

[26]  N. Grishin,et al.  Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily. , 2000, Structure.

[27]  D. Santi,et al.  The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Rasche,et al.  Mechanism for the enzymatic formation of 4-(beta-D-ribofuranosyl)aminobenzene 5'-phosphate during the biosynthesis of methanopterin. , 1998, Biochemistry.

[29]  C. Sander,et al.  Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases , 1993, Protein science : a publication of the Protein Society.