The crystal structure of a bacterial, bifunctional 5, 10 methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase

Shen, Betty; Dyer, David H.; D'Ari, Linda; Rabinowitz, Jesse C.; Stoddard, Barry

doi:10.1110/ps.8.6.1342

Cited by 32 publications

(40 citation statements)

References 31 publications

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“…Among the missing genes are those encoding methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase (FolD) and methionyl-tRNA formyltransferase (Fmt). FolD is a bifunctional enzyme that catalyzes sequentially (and reversibly) the oxidation of N 5 ,N 10 -methylenetetrahydrofolate to N 5 ,N 10 -methenyltetrahydrofolate and the hydrolysis of N 5 ,N 10 -methenyltetrahydrofolate to N 10 -formyltetrahydrofolate (Shen et al 1999;Eadsforth et al 2012). These two functions permit N 5 ,N 10 -methylenetetrahydrofolate to supply one-carbon units for the synthesis of carbons 2 and 8 of purines and the formyl group of N-formylmethionyl-tRNA (f) .…”

Section: One-carbon Transfer Reactionsmentioning

confidence: 99%

Phytoplasma Genomes: Evolution Through Mutually Complementary Mechanisms, Gene Loss and Horizontal Acquisition

Zhao

Davis

Wei

et al. 2014

Genomics of Plant-Associated Bacteria

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Section: One-carbon Transfer Reactionsmentioning

confidence: 99%

Phytoplasma Genomes: Evolution Through Mutually Complementary Mechanisms, Gene Loss and Horizontal Acquisition

Zhao

Davis

Wei

et al. 2014

Genomics of Plant-Associated Bacteria

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“…The DC domain of the human NADP-dependent DCS structure has been solved with NADP (10) and with NADP and three different folate analogues (11). The E. coli NADP-dependent DC structure has been solved in the absence of ligands (12). The S. cerevisiae NAD-dependent dehydrogenase has been solved both without ligands and in complex with NAD (13).…”

Section: Construction Of the Homology Model Of Human Nmdmc-crystalmentioning

confidence: 99%

“…The structure of the Escherichia coli NADPdependent DC has been determined by x-ray crystallography in the absence of bound substrates (12), and the structure of the Saccharomyces cerevisiae NAD-dependent dehydrogenase has been determined with and without bound NAD (13). However, since no crystal structure of NMDMC has yet been obtained, we constructed a homology model of the enzyme based on three related structures and used this to locate the P i and Mg 2ϩ binding sites using site-directed mutagenesis.…”

mentioning

confidence: 99%

Magnesium and Phosphate Ions Enable NAD Binding to Methylenetetrahydrofolate Dehydrogenase-Methenyltetrahydrofolate Cyclohydrolase

Christensen

Mirza

Berghuis

et al. 2005

Journal of Biological Chemistry

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The mitochondrial NAD-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase (NMDMC) is believed to have evolved from a trifunctional NADP-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase-synthetase. It is unique in its absolute requirement for inorganic phosphate and magnesium ions to support dehydrogenase activity. To enable us to investigate the roles of these ions, a homology model of human NMDMC was constructed based on the structures of three homologous proteins. The model supports the hypothesis that the absolutely required P i can bind in close proximity to the 2-hydroxyl of During embryogenesis and tumorigenesis mammalian mitochondria use a folate-dependent pathway to generate both glycine and one-carbon units to support cytoplasmic purine synthesis (1, 2). One of the enzymes in this pathway, the NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase (NMDMC), 5 catalyzes the interconversion of 5,10-methylenetetrahydrofolate (methylene-THF) and 10-formyltetrahydrofolate (formyl-THF) in mammalian mitochondria. The mitochondrial formyl-THF is converted to formate by a monofunctional formyl-THF synthetase and is released to the cytoplasm for reconversion into formyl-THF to support purine biosynthesis (1). NMDMC can use both NAD and NADP as a cofactor in its dehydrogenase activity, although the maximal activity with NADP is only about twenty percent of that with NAD (3). NMDMC is thought to have evolved from a trifunctional NADP-dependent methylene-THF dehydrogenase-methenyl-THF cyclohydrolase-formyl-THF synthetase (DCS) through the loss of the synthetase domain and the change in cofactor specificity from NADP to NAD (4). This change in cofactor specificity is important because the use of NAD rather than NADP in mitochondria shifts the equilibrium of the reaction to favor the production of formyl-THF (5). The increased production of formyl-THF is required to meet the demand for glycine and purines during embryogenesis (1, 2, 6). However, it is not known how this cofactor specificity change was accomplished.NMDMC is unique in its absolute requirement for magnesium and inorganic phosphate ions for NAD-dependent dehydrogenase activity and magnesium ions for NADP-dependent dehydrogenase activity (3, 7). However, neither ion is essential for the cyclohydrolase activity. The role of these ions in the dehydrogenase activity is not clear. The sequence of binding of the cofactors and substrates to NMDMC, as established kinetically by Yang and Mackenzie (3) and Rios-Orlandi and MacKenzie (7), suggests a role for P i and Mg 2ϩ in the binding of the cofactor; the ions bind to the protein first, followed by NAD and then the folate substrate. A preferred order of binding of the ions was not established; either ion appears to be able to bind to the enzyme and affect the binding of the other. These results suggested a possible interaction between the two ions in the binding site. The observation that P i competitively inhibits the cofactor in NADP-dependent de...

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“…The first deletion identified included residues 67 to 70, with modifications of residues 71 to 73. Structural interpretation was based on the threedimensional model of FolD (29). The THF binding site is composed of residues conserved in both humans (2) and B. subtilis (Fig.…”

mentioning

confidence: 99%

Mutations in Three Distinct Loci Cause Resistance to Peptide Deformylase Inhibitors inBacillus subtilis

Duroc

Giglione

Meinnel

2009

Antimicrob Agents Chemother

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Bacillus subtilis mutants with resistance against peptide deformylase inhibitors were isolated. All showed a bypass of the pathway through mutations in three genes required for formylation of Met-tRNA fMet , fmt, folD, and glyA. glyA corresponds to a yet uncharacterized locus inducing resistance. The bypass of formylation caused robust fitness reduction but was not accompanied by alterations of the transcription profile. A subtle adaptation of the enzymes of the intermediary metabolism was observed.In bacteria, all newly synthesized polypeptides transiently carry a formylated N terminus (1,18,33). Peptide deformylase (PDF) catalyzes the subsequent removal of the formyl group, and its gene is essential (11,22,23). The natural compound actinonin was the first PDF inhibitor (PDFI) characterized (4, 6, 8). Mechanisms causing PDFI resistance involve (i) mutations in the target gene, (ii) bypassing of the formylation pathway, or (iii) efflux of PDFI (4,9,10,15,17,19,20,25,31). Bacillus subtilis has two functional PDF genes, def and ykrB (14). The mechanisms of resistance have been studied only in bacteria expressing one active PDF gene. No analysis has approached the implications beyond the fitness cost often associated with PDFI resistance.To isolate variants resistant to PDFI, 100 l of an exponential-phase B. subtilis culture was plated onto Mueller-Hinton (MH) agar supplemented with 12 g/ml of actinonin. The plates were incubated for 2 days at 37°C, after which resistant colonies were restreaked and isolated. Cells were also plated

show abstract

The crystal structure of a bacterial, bifunctional 5, 10 methylene‐tetrahydrofolate dehydrogenase/cyclohydrolase

Cited by 32 publications

References 31 publications

Phytoplasma Genomes: Evolution Through Mutually Complementary Mechanisms, Gene Loss and Horizontal Acquisition

Phytoplasma Genomes: Evolution Through Mutually Complementary Mechanisms, Gene Loss and Horizontal Acquisition

Magnesium and Phosphate Ions Enable NAD Binding to Methylenetetrahydrofolate Dehydrogenase-Methenyltetrahydrofolate Cyclohydrolase

Mutations in Three Distinct Loci Cause Resistance to Peptide Deformylase Inhibitors inBacillus subtilis

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