guanosine-triphosphate and molybdenum-cofactor

The radical SAM (S-adenosyl-l-methionine) superfamily is one of the largest group of enzymes with >113000 annotated sequences [Landgraf, B. J., et al. (2016) Annu. Rev. Biochem. 85, 485-514]. Members of this superfamily catalyze the reductive cleavage of SAM using an oxygen sensitive 4Fe-4S cluster to transiently generate 5'-deoxyadenosyl radical that is subsequently used to initiate diverse free radical-mediated reactions. Because of the unique reactivity of free radicals, radical SAM enzymes frequently catalyze chemically challenging reactions critical for the biosynthesis of unique structures of cofactors and natural products. In this Perspective, I will discuss the impact of characterizing novel functions in radical SAM enzymes on our understanding of biosynthetic pathways and use two recent examples from my own group with a particular emphasis on two radical SAM enzymes that are responsible for carbon skeleton formation during the biosynthesis of a cofactor and natural products.

Topics: Biological Products; Carbon-Carbon Lyases; Coenzymes; Crystallography, X-Ray; Escherichia coli Proteins; Guanosine Triphosphate; Humans; Isomerases; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum Cofactors; Nuclear Proteins; Organophosphorus Compounds; Protein Conformation; Pteridines; Pterins; Recombinant Proteins; S-Adenosylmethionine

The first step in the biosynthesis of the molybdopterin cofactor involves an unprecedented insertion of the purine C8 carbon between the C2' and C3' carbons of the ribose moiety of GTP. Here we review mechanistic studies on this remarkable transformation. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.

Topics: Biocatalysis; Carbon; Coenzymes; Escherichia coli Proteins; Guanosine Triphosphate; Humans; Isomerases; Metalloproteins; Molybdenum Cofactors; Pteridines; Purines; Ribose

The molybdenum cofactor (Moco) is an essential redox cofactor found in all kingdoms of life. Genetic mutations in the human Moco biosynthetic enzymes lead to a fatal metabolic disorder, Moco deficiency (MoCD). Greater than 50% of all human MoCD patients have mutations in MOCS1A, a radical S-adenosyl-l-methionine (SAM) enzyme involved in the conversion of guanosine 5'-triphosphate (GTP) into cyclic pyranopterin monophosphate. In MOCS1A, one of the frequently affected locations is the GG motif constituted of two consecutive Gly at the C-terminus. The GG motif is conserved among all MOCS1A homologues, but its role in catalysis or the mechanism by which its mutation causes MoCD was unknown. Here, we report the functional characterization of the GG motif using MoaA, a bacterial homologue of MOCS1A, as a model. Our study elucidated that the GG motif is essential for the activity of MoaA to produce 3',8-cH2GTP from GTP (GTP 3',8-cyclase), and that synthetic peptides corresponding to the C-terminal region of wt-MoaA rescue the GTP 3',8-cyclase activity of the GG-motif mutants. Further biochemical characterization suggested that the C-terminal tail containing the GG motif interacts with the SAM-binding pocket of MoaA, and is essential for the binding of SAM and subsequent radical initiation. In sum, these observations suggest that the C-terminal tail of MoaA provides an essential mechanism to trigger the free radical reaction, impairment of which results in the complete loss of catalytic function of the enzyme, and causes MoCD.

Topics: Amino Acid Motifs; Binding Sites; Carbon-Carbon Lyases; Coenzymes; Escherichia coli; Glycine; Guanosine Triphosphate; Hydrogen; Hydrolases; Kinetics; Metalloproteins; Molybdenum Cofactors; Mutation; Nuclear Proteins; Protein Conformation; Pteridines

MoaA is a radical S-adenosylmethionine (AdoMet) enzyme that catalyzes a complex rearrangement of guanosine-5'-triphosphate (GTP) in the first step of molybdopterin biosynthesis. In this paper, we provide additional characterization of the MoaA reaction product, describe the use of 2'-chloroGTP to trap the GTP C3' radical, generated by hydrogen atom transfer to the 5'-deoxyadenosyl radical, and the use of 2'-deoxyGTP to block a late step in the reaction sequence. These probes, coupled with the previously reported trapping of an intermediate in which C3' of the ribose is linked to C8 of the purine, allow us to propose a plausible mechanism for the MoaA-catalyzed reaction.

Topics: Coenzymes; Escherichia coli; Escherichia coli Proteins; Guanosine Triphosphate; Halogenation; Isomerases; Metalloproteins; Molybdenum Cofactors; Pteridines; Substrate Specificity

MoaA/MoaC catalyze a remarkable rearrangement reaction in which guanosine-5'-triphosphate (GTP) is converted to cyclic pyranopterin monophosphate (cPMP). In this reaction, the C8 of GTP is inserted between the C2' and the C3' carbons of the GTP ribose. Previous experiments with GTP isotopomers demonstrated that the ribose C3' hydrogen atom is abstracted by the adenosyl radical. This led to a novel mechanistic proposal involving an intermediate with a bond between the C8 of guanine and C3' of the ribose. This paper describes the use of 2',3'-dideoxyGTP to trap this intermediate.

Topics: Biocatalysis; Coenzymes; Guanosine Triphosphate; Hydrolases; Metalloproteins; Molybdenum Cofactors; Pteridines; Ribose

MoaA, a radical S-adenosylmethionine enzyme, catalyzes the first step in molybdopterin biosynthesis. This reaction involves a complex rearrangement in which C8 of guanosine triphosphate is inserted between C2' and C3' of the ribose. This study identifies the site of initial hydrogen atom abstraction by the adenosyl radical and advances a mechanistic proposal for this unprecedented reaction.

Topics: Carbon; Catalysis; Coenzymes; Guanosine Triphosphate; Hydrolases; Magnetic Resonance Spectroscopy; Metalloproteins; Models, Chemical; Molybdenum Cofactors; Pteridines; Ribose; Spectrometry, Mass, Electrospray Ionization

The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S-adenosylmethionine-dependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S-adenosylmethionine using an Fe-S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein-ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein-ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism.

Topics: Amino Acid Sequence; Apoproteins; Bacterial Proteins; Binding Sites; Coenzymes; Conserved Sequence; Crystallography, X-Ray; Guanosine Triphosphate; Metalloproteins; Models, Molecular; Molecular Sequence Data; Molybdenum Cofactors; Protein Binding; Protein Structure, Quaternary; Protein Structure, Tertiary; Pteridines; Sequence Alignment; Thermus thermophilus

The first step in molybdenum cofactor biosynthesis, the conversion of 5'-GTP to precursor Z, an oxygen-sensitive tetrahydropyranopterin is catalyzed by the S-adenosylmethionine (SAM)-dependent enzyme MoaA and the accessory protein MoaC. This reaction involves the radical-initiated intramolecular rearrangement of the guanine C8 atom. MoaA harbors an N-terminal [4Fe-4S] cluster, which is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical (5'-dA*), and a C-terminal [4Fe-4S] cluster presumably involved in substrate binding and/or activation. Biochemical studies identified residues involved in 5'-GTP binding and the determinants of nucleotide specificity. The crystal structure of MoaA in complex with 5'-GTP confirms the biochemical data and provides valuable insights into the subsequent radical reaction. MoaA binds 5'-GTP with high affinity and interacts through its C-terminal [4Fe-4S] cluster with the guanine N1 and N2 atoms, in a yet uncharacterized binding mode. The tightly anchored triphosphate moiety prevents the escape of radical intermediates. This structure also visualizes the L-Met and 5'-dA cleavage products of SAM. Rotation of the 5'-dA ribose and/or conformational changes of the guanosine are proposed to bring the 5'-deoxyadenosyl radical into close proximity of either the ribose C2' and C3' or the guanine C8 carbon atoms leading to hydrogen abstraction.

Topics: Binding Sites; Coenzymes; Crystallography, X-Ray; Guanosine Triphosphate; Hydrolases; Iron-Sulfur Proteins; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum Cofactors; Protein Conformation; Pteridines; S-Adenosylmethionine; Staphylococcus aureus

A universal molybdenum-containing cofactor (MoCo) is essential for the activity of all human molybdoenzymes, including sulphite oxidase. The free cofactor is highly unstable, and all organisms share a similar biosynthetic pathway. The involved enzymes exhibit homologies, even between bacteria and humans. We have exploited these homologies to isolate a cDNA for the heterodimeric molybdopterin (MPT)-synthase. This enzyme is necessary for the conversion of an unstable precursor into molybdopterin, the organic moiety of MoCo. The corresponding transcript shows a bicistronic structure, encoding the small and large subunits of the MPT-synthase in two different open reading frames (ORFs) that overlap by 77 nucleotides. In various human tissues, only one size of mRNA coinciding with the bicistronic transcript was detected. In vitro translation and mutagenesis experiments demonstrated that each ORF is translated independently, leading to the synthesis of a 10-kDa protein and a 21-kDa protein for the small and large subunits, respectively, and indicated that the 3'-proximal ORF of the bicistronic transcript is translated by leaky scanning.

Topics: Amino Acid Sequence; Animals; Base Sequence; Blotting, Northern; Coenzymes; Escherichia coli; Gene Library; Genes, Overlapping; Guanosine Triphosphate; Humans; Liver; Metalloproteins; Molecular Sequence Data; Molybdenum Cofactors; Mutagenesis, Insertional; Protein Biosynthesis; Pteridines; Rabbits; Reading Frames; Reticulocytes; Sequence Homology, Amino Acid; Sulfurtransferases

All molybdoenzyme activities are absent in chlB mutants because of their inability to synthesize molybdopterin guanine dinucleotide, which together with molybdate constitutes the molybdenum cofactor in Escherichia coli. The chlB mutants are able to synthesize molybdopterin. We have previously shown that the inactive nitrate reductase present in a chlB mutant can be activated in a process requiring protein FA and a heat-stable low-molecular-weight substance. We show here that purified nitrate reductase from the soluble fraction of a chlB mutant can be partially activated in a process that requires protein FA, GTP, and an additional protein termed factor X. It appears that the molybdopterin present in the nitrate reductase of a chlB mutant is converted to molybdopterin guanine dinucleotide during activation. The activation is absolutely dependent upon both protein FA and factor X. Factor X activity is present in chlA, chlB, chlE, and chlG mutants.

Topics: Bacterial Proteins; Chlorates; Coenzymes; Drug Resistance, Microbial; Enzyme Activation; Escherichia coli; Guanosine Triphosphate; Kinetics; Metalloproteins; Molecular Weight; Molybdenum Cofactors; Mutation; Nitrate Reductase; Nitrate Reductases; Pteridines; Spectrometry, Fluorescence