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1.
ChemistryOpen ; 12(5): e202300052, 2023 05.
Article in English | MEDLINE | ID: mdl-37129313

ABSTRACT

Methylenetetrahydrofolate dehydrogenase (MTHFD2) is a mitochondrial enzyme involved in 1 C metabolism that is upregulated in various cancer cells, but absent in normal proliferating cells. Xanthine derivatives are the first selective inhibitors of MTHFD2 which bind to its allosteric site. Xanthine derivatives (including the co-crystallized inhibitors) were herein interrogated by molecular/induced-fit docking, MM-GBSA binding free energy calculations and molecular dynamics simulations in both MTHFD2 and MTHFD1 (a close homolog expressed in healthy cells). The gained insights from our in silico protocol allowed us to study binding mode, key protein-ligand interactions and dynamic movement of the allosteric inhibitors, correlating with their experimental binding affinities, biological activities and selectivity for MTHFD2. The reported conformational changes with MTHFD2 upon binding of xanthine derivatives were furthermore evaluated and confirmed by RMSF analyses of the MD simulation trajectories. The results reported herein are expected to benefit in the rational design of selective MTHFD2 allosteric inhibitors.


Subject(s)
Methylenetetrahydrofolate Dehydrogenase (NADP) , Molecular Dynamics Simulation , Allosteric Site , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Xanthine , Molecular Docking Simulation
2.
ChemMedChem ; 17(18): e202200274, 2022 09 16.
Article in English | MEDLINE | ID: mdl-35712863

ABSTRACT

Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is a mitochondrial 1-carbon metabolism enzyme, which is an attractive anticancer drug target as it is highly upregulated in cancer but is not expressed in healthy adult cells. Selective MTHFD2 inhibitors could therefore offer reduced side-effects during treatment, which are common with antifolate drugs that target other 1C-metabolism enzymes. This task is challenging however, as MTHFD2 shares high sequence identity with the constitutively expressed isozymes cytosolic MTHFD1 and mitochondrial MTHFD2L. In fact, one of the most potent MTHFD2 inhibitors reported to date, TH7299, is actually more active against MTHFD1 and MTHFD2L. While structures of MTHFD2 and MTHFD1 exist, no MTHFD2L structures are available. We determined the first structure of MTHFD2L and its complex with TH7299, which reveals the structural basis for its highly potent MTHFD2L inhibition. Detailed analysis of the MTHFD2L structure presented here clearly highlights the challenges associated with developing truly isoform-selective MTHFD2 inhibitors.


Subject(s)
Antineoplastic Agents , Folic Acid Antagonists , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Carbon , Humans , Isoenzymes/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism
3.
PLoS Comput Biol ; 18(5): e1010140, 2022 05.
Article in English | MEDLINE | ID: mdl-35613161

ABSTRACT

Methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) is a new drug target that is expressed in cancer cells but not in normal adult cells, which provides an Achilles heel to selectively kill cancer cells. Despite the availability of crystal structures of MTHFD2 in the inhibitor- and cofactor-bound forms, key information is missing due to technical limitations, including (a) the location of absolutely required Mg2+ ion, and (b) the substrate-bound form of MTHFD2. Using computational modeling and simulations, we propose that two magnesium ions are present at the active site whereby (i) Arg233, Asp225, and two water molecules coordinate [Formula: see text], while [Formula: see text] together with Arg233 stabilize the inorganic phosphate (Pi); (ii) Asp168 and three water molecules coordinate [Formula: see text], and [Formula: see text] further stabilizes Pi by forming a hydrogen bond with two oxygens of Pi; (iii) Arg201 directly coordinates the Pi; and (iv) through three water-mediated interactions, Asp168 contributes to the positioning and stabilization of [Formula: see text], [Formula: see text] and Pi. Our computational study at the empirical valence bond level allowed us also to elucidate the detailed reaction mechanisms. We found that the dehydrogenase activity features a proton-coupled electron transfer with charge redistribution connected to the reorganization of the surrounding water molecules which further facilitates the subsequent cyclohydrolase activity. The cyclohydrolase activity then drives the hydration of the imidazoline ring and the ring opening in a concerted way. Furthermore, we have uncovered that two key residues, Ser197/Arg233, are important factors in determining the cofactor (NADP+/NAD+) preference of the dehydrogenase activity. Our work sheds new light on the structural and kinetic framework of MTHFD2, which will be helpful to design small molecule inhibitors that can be used for cancer treatment.


Subject(s)
Aminohydrolases , Methylenetetrahydrofolate Dehydrogenase (NADP) , Aminohydrolases/chemistry , Aminohydrolases/metabolism , Kinetics , Magnesium , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Mitochondria/metabolism , Water
4.
PLoS One ; 15(5): e0232959, 2020.
Article in English | MEDLINE | ID: mdl-32401802

ABSTRACT

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.


Subject(s)
Cloning, Molecular/methods , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Thermus thermophilus/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Crystallography, X-Ray , Enzyme Stability , Models, Molecular , Molecular Dynamics Simulation , Principal Component Analysis , Protein Structure, Secondary , Thermodynamics , Thermus thermophilus/genetics
5.
FEBS Open Bio ; 9(4): 618-628, 2019 04.
Article in English | MEDLINE | ID: mdl-30984537

ABSTRACT

The enzyme 5,10-methylenetetrahydrofolate dehydrogenase (MTHFD) is essential for the production of certain amino acids (glycine, serine, and methionine) and nucleic acids (thymidylate and purine). Here, we identified a cDNA encoding this enzyme from the silkworm Bombyx mori. The recombinant B. mori MTHFD (bmMTHFD) expressed in Escherichia coli recognized 5,10-methylenetetrahydrofolate and 5,10-methenyltetrahydrofolate as substrate in the presence of NADP + as well as NAD +. The bmMTHFD structure was determined at a resolution of 1.75 Å by X-ray crystallography. Site-directed mutagenesis indicated that the amino acid residue Tyr49 contributed to its catalytic activity. Our findings provide insight into the mechanism underlying the activity of MTHFD from B. mori and potentially other insects and may therefore facilitate the development of inhibitors specific to MTHFD as insecticides.


Subject(s)
Bombyx/genetics , Insect Proteins/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Amino Acid Sequence , Animals , Bombyx/enzymology , Bombyx/metabolism , DNA, Complementary/chemistry , DNA, Complementary/genetics , DNA, Complementary/metabolism , Escherichia coli/genetics , Insect Proteins/chemistry , Insect Proteins/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Molecular Structure , Mutagenesis, Site-Directed , Phylogeny , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment
6.
Acta Crystallogr F Struct Biol Commun ; 75(Pt 3): 148-152, 2019 Mar 01.
Article in English | MEDLINE | ID: mdl-30839287

ABSTRACT

The enzymes involved in folate metabolism are key drug targets for cell-growth modulation, and accurate crystallographic structures provide templates to be exploited for structure-based ligand design. In this context, three ternary complex structures of human methylenetetrahydrofolate dehydrogenase/cyclohydrolase have been published [Schmidt et al. (2000), Biochemistry, 39, 6325-6335] and potentially represent starting points for the development of new antifolate inhibitors. However, an inspection of the models and the deposited data revealed deficiencies and raised questions about the validity of the structures. A number of inconsistencies relating to the publication were also identified. Additional refinement was carried out with the deposited data, seeking to improve the models and to then validate the complex structures or correct the record. In one case, the inclusion of the inhibitor in the structure was supported and alterations to the model allowed details of enzyme-ligand interactions to be described that had not previously been discussed. For one weak inhibitor, the data suggested that the ligand may adopt two poses in the binding site, both with few interactions with the enzyme. In the third case, that of a potent inhibitor, inconsistencies were noted in the assignment of the chemical structure and there was no evidence to support the inclusion of the ligand in the active site.


Subject(s)
Hydrolases/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Binding Sites , Crystallography, X-Ray , Folic Acid Antagonists/chemistry , Humans , Hydrogen Bonding , Ligands , Protein Conformation
7.
Cancer Res ; 77(4): 937-948, 2017 02 15.
Article in English | MEDLINE | ID: mdl-27899380

ABSTRACT

To sustain their proliferation, cancer cells become dependent on one-carbon metabolism to support purine and thymidylate synthesis. Indeed, one of the most highly upregulated enzymes during neoplastic transformation is MTHFD2, a mitochondrial methylenetetrahydrofolate dehydrogenase and cyclohydrolase involved in one-carbon metabolism. Because MTHFD2 is expressed normally only during embryonic development, it offers a disease-selective therapeutic target for eradicating cancer cells while sparing healthy cells. Here we report the synthesis and preclinical characterization of the first inhibitor of human MTHFD2. We also disclose the first crystal structure of MTHFD2 in complex with a substrate-based inhibitor and the enzyme cofactors NAD+ and inorganic phosphate. Our work provides a rationale for continued development of a structural framework for the generation of potent and selective MTHFD2 inhibitors for cancer treatment. Cancer Res; 77(4); 937-48. ©2017 AACR.


Subject(s)
Enzyme Inhibitors/chemistry , Methenyltetrahydrofolate Cyclohydrolase/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Mitochondria/enzymology , Binding Sites , Crystallization , Folic Acid/analogs & derivatives , Folic Acid/metabolism , Humans , Leucovorin/analogs & derivatives , Leucovorin/metabolism , Methenyltetrahydrofolate Cyclohydrolase/antagonists & inhibitors , Methylenetetrahydrofolate Dehydrogenase (NADP)/antagonists & inhibitors , Minor Histocompatibility Antigens , NAD/metabolism , Protein Multimerization
8.
Microbiology (Reading) ; 162(1): 145-155, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26531681

ABSTRACT

Most organisms possess bifunctional FolD [5,10-methylenetetrahydrofolate (5,10-CH2-THF) dehydrogenase-cyclohydrolase] to generate NADPH and 10-formyltetrahdrofolate (10-CHO-THF) required in various metabolic steps. In addition, some organisms including Clostridium perfringens possess another protein, Fhs (formyltetrahydrofolate synthetase), to synthesize 10-CHO-THF. Here, we show that unlike the bifunctional FolD of Escherichia coli (EcoFolD), and contrary to its annotated bifunctional nature, C. perfringens FolD (CpeFolD) is a monofunctional 5,10-CH2-THF dehydrogenase. The dehydrogenase activity of CpeFolD is about five times more efficient than that of EcoFolD. The 5,10-methenyltetrahydrofolate (5,10-CH+-THF) cyclohydrolase activity in C. perfringens is provided by another protein, FchA (5,10-CH+-THF cyclohydrolase), whose cyclohydrolase activity is ∼ 10 times more efficient than that of EcoFolD. Kinetic parameters for CpeFhs were also determined for utilization of all of its substrates. Both CpeFolD and CpeFchA are required to substitute for the single bifunctional FolD in E. coli. The simultaneous presence of CpeFolD and CpeFchA is also necessary to rescue an E. coli folD deletion strain (harbouring CpeFhs support) for its formate and glycine auxotrophies, and to alleviate its susceptibility to trimethoprim (an antifolate drug) or UV light. The presence of the three clostridial proteins (FolD, FchA and Fhs) is required to maintain folate homeostasis in the cell.


Subject(s)
Clostridium perfringens/enzymology , Escherichia coli/enzymology , Formate-Tetrahydrofolate Ligase/metabolism , Methenyltetrahydrofolate Cyclohydrolase/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Amino Acid Sequence , Clostridium perfringens/chemistry , Clostridium perfringens/genetics , Escherichia coli/chemistry , Escherichia coli/genetics , Formate-Tetrahydrofolate Ligase/chemistry , Formate-Tetrahydrofolate Ligase/genetics , Kinetics , Methenyltetrahydrofolate Cyclohydrolase/chemistry , Methenyltetrahydrofolate Cyclohydrolase/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Molecular Sequence Data , Sequence Alignment
9.
J Med Chem ; 58(20): 7938-48, 2015 Oct 22.
Article in English | MEDLINE | ID: mdl-26322631

ABSTRACT

The bifunctional enzyme N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclo hydrolase (FolD) is essential for growth in Trypanosomatidae. We sought to develop inhibitors of Trypanosoma brucei FolD (TbFolD) as potential antiparasitic agents. Compound 2 was synthesized, and the molecular structure was unequivocally assigned through X-ray crystallography of the intermediate compound 3. Compound 2 showed an IC50 of 2.2 µM, against TbFolD and displayed antiparasitic activity against T. brucei (IC50 49 µM). Using compound 2, we were able to obtain the first X-ray structure of TbFolD in the presence of NADP(+) and the inhibitor, which then guided the rational design of a new series of potent TbFolD inhibitors.


Subject(s)
Phenylurea Compounds/chemical synthesis , Phenylurea Compounds/pharmacology , Pyrimidinones/chemical synthesis , Pyrimidinones/pharmacology , Trypanocidal Agents/chemical synthesis , Trypanocidal Agents/pharmacology , Trypanosoma brucei brucei/drug effects , Animals , Crystallography, X-Ray , Drug Design , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/therapeutic use , Humans , Leukemia/drug therapy , Macrophages/drug effects , Methylenetetrahydrofolate Dehydrogenase (NADP)/antagonists & inhibitors , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Models, Molecular , Structure-Activity Relationship , Trypanosoma brucei brucei/enzymology , Trypanosoma brucei brucei/growth & development , Trypanosomiasis, African/drug therapy , Trypanosomiasis, African/parasitology
10.
Mol Cancer Res ; 13(10): 1361-6, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26101208

ABSTRACT

Rapidly proliferating tumors attempt to meet the demands for nucleotide biosynthesis by upregulating folate pathways that provide the building blocks for pyrimidine and purine biosynthesis. In particular, the key role of mitochondrial folate enzymes in providing formate for de novo purine synthesis and for providing the one-carbon moiety for thymidylate synthesis has been recognized in recent studies. We have shown a significant correlation between the upregulation of the mitochondrial folate enzymes, high proliferation rates, and sensitivity to the folate antagonist methotrexate (MTX). Burkitt lymphoma and diffuse large-cell lymphoma tumor specimens have the highest levels of mitochondrial folate enzyme expression and are known to be sensitive to treatment with MTX. A key enzyme upregulated in rapidly proliferating tumors but not in normal adult cells is the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase (MTHFD2). This perspective outlines the rationale for specific targeting of MTHFD2 and compares known and generated crystal structures of MTHFD2 and closely related enzymes as a molecular basis for developing therapeutic agents against MTHFD2. Importantly, the development of selective inhibitors of mitochondrial methylenetetrahydrofolate dehydrogenase is expected to have substantial activity, and this perspective supports the investigation and development of MTHFD2 inhibitors for anticancer therapy.


Subject(s)
Aminohydrolases/biosynthesis , Methylenetetrahydrofolate Dehydrogenase (NADP)/biosynthesis , Mitochondria/enzymology , Multienzyme Complexes/biosynthesis , Neoplasms/drug therapy , Neoplasms/enzymology , Aminohydrolases/chemistry , Aminohydrolases/metabolism , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Cell Proliferation/drug effects , Cell Proliferation/physiology , Drug Design , Humans , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Mice , Models, Molecular , Molecular Targeted Therapy , Multienzyme Complexes/chemistry , Multienzyme Complexes/metabolism , Neoplasms/pathology , Protein Conformation , Protein Folding , Structure-Activity Relationship
11.
Proc Natl Acad Sci U S A ; 112(2): 400-5, 2015 Jan 13.
Article in English | MEDLINE | ID: mdl-25548164

ABSTRACT

An inborn error of metabolism associated with mutations in the human methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) gene has been identified. The proband presented with SCID, megaloblastic anemia, and neurologic abnormalities, but the causal metabolic impairment is unknown. SCID has been associated with impaired purine nucleotide metabolism, whereas megaloblastic anemia has been associated with impaired de novo thymidylate (dTMP) biosynthesis. MTHFD1 functions to condense formate with tetrahydrofolate and serves as the primary entry point of single carbons into folate-dependent one-carbon metabolism in the cytosol. In this study, we examined the impact of MTHFD1 loss of function on folate-dependent purine, dTMP, and methionine biosynthesis in fibroblasts from the proband with MTHFD1 deficiency. The flux of formate incorporation into methionine and dTMP was decreased by 90% and 50%, respectively, whereas formate flux through de novo purine biosynthesis was unaffected. Patient fibroblasts exhibited enriched MTHFD1 in the nucleus, elevated uracil in DNA, lower rates of de novo dTMP synthesis, and increased salvage pathway dTMP biosynthesis relative to control fibroblasts. These results provide evidence that impaired nuclear de novo dTMP biosynthesis can lead to both megaloblastic anemia and SCID in MTHFD1 deficiency.


Subject(s)
Methylenetetrahydrofolate Dehydrogenase (NADP)/deficiency , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Mutant Proteins/genetics , Mutant Proteins/metabolism , Thymidine Monophosphate/biosynthesis , Amino Acid Substitution , Anemia, Megaloblastic/genetics , Anemia, Megaloblastic/metabolism , Cell Line , Cell Nucleus/metabolism , Codon, Nonsense , DNA Damage , Fibroblasts/metabolism , Humans , Metabolic Networks and Pathways , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Minor Histocompatibility Antigens , Mutant Proteins/chemistry , Phenotype , Point Mutation , Severe Combined Immunodeficiency/genetics , Severe Combined Immunodeficiency/metabolism
12.
Hum Mutat ; 35(1): 96-104, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24123340

ABSTRACT

Maternal folate levels and polymorphisms in folate-related genes are known risk factors for neural tube defects (NTDs). SNPs in the mitochondrial folate gene MTHFD1L are associated with the risk of NTDs. We investigated whether different alleles of SNP rs7646 in the 3' UTR of MTHFD1L can be differentially regulated by microRNAs affecting MTHFD1L expression. We previously reported that miR-9 targets MTHFD1L and now we identify miR-197 as an additional miRNA regulator. Both of these miRNAs have predicted binding sites in the MTHFD1L 3' UTR in the region containing SNP rs7646. We have determined whether the alleles of SNP rs7646 (A/G) and miRNA expression levels affect miRNA binding preferences for the MTHFD1L 3' UTR and consequently MTHFD1L expression. Our results indicate that miR-9 and miR-197 specifically downregulate MTHFD1L levels in HEK293 and MCF-7 cells and that SNPrs7646 significantly affects miR-197 binding affinity to the MTHFD1L 3' UTR, causing more efficient posttranscriptional gene repression in the presence of the allele that is associated with increased risk of NTDs. These results reveal that the association of SNP rs7646 and NTD risk involves differences in microRNA regulation and, highlights the importance of genotype-dependent differential microRNA regulation in relation to human disease risk.


Subject(s)
3' Untranslated Regions , Aminohydrolases/genetics , Aminohydrolases/metabolism , Formate-Tetrahydrofolate Ligase/genetics , Formate-Tetrahydrofolate Ligase/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , MicroRNAs/metabolism , Multienzyme Complexes/genetics , Multienzyme Complexes/metabolism , Neural Tube Defects/genetics , Alleles , Aminohydrolases/chemistry , Binding Sites , Formate-Tetrahydrofolate Ligase/chemistry , Gene Expression Regulation , Genetic Predisposition to Disease , Genetic Variation , Genotype , HEK293 Cells , Humans , MCF-7 Cells , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , MicroRNAs/chemistry , Models, Molecular , Multienzyme Complexes/chemistry , Neural Tube Defects/metabolism , Polymorphism, Single Nucleotide , Thermodynamics
13.
FEBS J ; 279(23): 4350-60, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23050773

ABSTRACT

The bifunctional N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram-negative pathogen Acinetobacter baumanni and determined high-resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed.


Subject(s)
Acinetobacter baumannii/enzymology , Acinetobacter baumannii/metabolism , Bacterial Proteins/metabolism , Folic Acid/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Bacterial Proteins/chemistry , Crystallography, X-Ray , Folic Acid/chemistry , Kinetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Protein Structure, Secondary
14.
Mol Biochem Parasitol ; 181(2): 178-85, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22108435

ABSTRACT

Three enzyme activities in the protozoan Leishmania major, namely N(5),N(10)-methylenetetrahydrofolate dehydrogenase/N(5),N(10)-methenyltetrahydrofolate cyclohydrolase (DHCH) and N(10)-formyltetrahydrofolate ligase (FTL) produce the essential intermediate N(10)-formyltetrahydrofolate. Although trypanosomatids possess at least one functional DHCH, the same is not true for FTL, which is absent in Trypanosoma brucei. Here, we present the 2.7 Å resolution crystal structure of the bifunctional apo-DHCH from L. major, which is a potential drug target. Sequence alignments show that the cytosolic enzymes found in trypanosomatids share a high level of identity of approximately 60%. Additionally, residues that interact and participate in catalysis in the human homologue are conserved amongst trypanosomatid sequences and this may complicate attempts to derive potent, parasite specific DHCH inhibitors.


Subject(s)
Leishmania major/enzymology , Methenyltetrahydrofolate Cyclohydrolase/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Protozoan Proteins/chemistry , Amino Acid Sequence , Antiprotozoal Agents/pharmacology , Enzyme Activation/drug effects , Humans , Methenyltetrahydrofolate Cyclohydrolase/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Protozoan Proteins/genetics , Sequence Homology , Sequence Homology, Amino Acid
15.
J Microbiol Biotechnol ; 18(2): 283-6, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18309272

ABSTRACT

The methylenetetrahydrofolate dehydrogenase/ cyclohydrolase (MTHFDC) from the thermoacidophilic archaeon Thermoplasma acidophilum is a 30.6 kDa molecular-mass enzyme that sequentially catalyzes the conversion of formyltetrahydrofolate to methylenetetrahydrofolate, with a preference for NADP as a cofactor, rather than NAD. In order to elucidate the functional and structural features of MTHFDC from archaeons at a molecular level, it was overexpressed in Escherichia coli and crystallized in the presence of its cofactor, NADP, at 295 K using polyethylene glycol (PEG) 4000 as a precipitant. The crystal is a member of the monoclinic space group P21, with the following unit cell parameters: a=66.333 A, b=52.868 A, c=86.099 A, and beta= 97.570o, and diffracts to a resolution of at least 2.40 A at the synchrotron. Assuming a dimer in the crystallographic asymmetric unit, the calculated Matthews parameter (VM) was 2.44 A3/Da and the solvent content was 49.7%.


Subject(s)
Aminohydrolases/chemistry , Archaeal Proteins/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Multienzyme Complexes/chemistry , Thermoplasma/enzymology , Aminohydrolases/metabolism , Archaeal Proteins/metabolism , Crystallization , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Multienzyme Complexes/metabolism , Thermoplasma/chemistry
16.
Arch Biochem Biophys ; 442(2): 196-205, 2005 Oct 15.
Article in English | MEDLINE | ID: mdl-16171773

ABSTRACT

A human mitochondrial isozyme of C1-tetrahydrofolate (THF) synthase was previously identified by its similarity to the human cytoplasmic C1-THF synthase. All C1-THF synthases characterized to date, from yeast to human, are trifunctional, containing the activities of 5,10-methylene-THF dehydrogenase, 5,10-methenyl-THF cyclohydrolase, and 10-formyl-THF synthetase. Here we report on the enzymatic characterization of the recombinant human mitochondrial isozyme. Enzyme assays of purified human mitochondrial C1-THF synthase protein revealed only the presence of 10-formyl-THF synthetase activity. Gel filtration and crosslinking studies indicated that human mitochondrial C1-THF synthase exists as a homodimer in solution. Steady-state kinetic characterization of the 10-formyl-THF synthetase activity was performed using (6R,S)-H4-PteGlu1, (6R,S)-H4-PteGlu3, and (6R,S)-H4-PteGlu5 substrates. The (6R,S)-H4-PteGlun Km dropped from greater than 500 microM for the monoglutamate to 15 microM and 3.6 microM for the tri- and pentaglutamates, respectively. The Km values for formate and ATP also are lowered when THF polyglutamates are used. The formate Km dropped 79-fold and the ATP Km dropped more than 5-fold when (6R,S)-H4-PteGlu5 was used as the substrate in place of (6R,S)-H4-PteGlu1.


Subject(s)
Aminohydrolases/chemistry , Formate-Tetrahydrofolate Ligase/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Mitochondria/enzymology , Multienzyme Complexes/chemistry , Aminohydrolases/genetics , Aminohydrolases/metabolism , Biological Assay/methods , Formate-Tetrahydrofolate Ligase/genetics , Formate-Tetrahydrofolate Ligase/metabolism , Glutamates/chemistry , Glutamates/metabolism , Humans , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Kinetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Multienzyme Complexes/genetics , Multienzyme Complexes/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity
17.
J Biol Chem ; 280(40): 34316-23, 2005 Oct 07.
Article in English | MEDLINE | ID: mdl-16100107

ABSTRACT

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 Pi can bind in close proximity to the 2'-hydroxyl of NAD through interactions with Arg166 and Arg198. The characterization of mutants of Arg166, Asp190, and Arg198 show that Arg166 is primarily responsible for Pi binding, while Arg198 plays a secondary role, assisting in binding and properly orienting the ion in the cofactor binding site. Asp190 helps to properly position Arg166. Mutants of Asp133 suggest that the magnesium ion interacts with both Pi and the aspartate side chain and plays a role in positioning Pi and NAD. NMDMC uses Pi and magnesium to adapt an NADP binding site for NAD binding. This adaptation represents a novel variation of the classic Rossmann fold.


Subject(s)
Aminohydrolases/chemistry , Aminohydrolases/metabolism , Magnesium/physiology , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/metabolism , Multienzyme Complexes/chemistry , Multienzyme Complexes/metabolism , NAD/metabolism , Phosphates/physiology , Amino Acid Sequence , Arginine , Binding Sites , Coenzymes , Escherichia coli/enzymology , Humans , Ions , Magnesium/chemistry , Models, Molecular , Molecular Sequence Data , Phosphates/chemistry , Protein Folding , Protein Structure, Tertiary , Saccharomyces cerevisiae/enzymology , Sequence Homology
18.
J Biol Chem ; 280(9): 7597-602, 2005 Mar 04.
Article in English | MEDLINE | ID: mdl-15611115

ABSTRACT

The Mthfd1 gene encoding the cytoplasmic methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase enzyme (DCS) was inactivated in embryonic stem cells. The null embryonic stem cells were used to generate spontaneously immortalized fibroblast cell lines that exhibit the expected purine auxotrophy. Elimination of these cytoplasmic activities allowed for the accurate assessment of similar activities encoded by other genes in these cells. A low level of 10-formyltetrahydrofolate synthetase was detected and was shown to be localized to mitochondria. However, NADP-dependent methylenetetrahydrofolate dehydrogenase activity was not detected. Northern blot analysis suggests that a recently identified mitochondrial DCS (Prasannan, P., Pike, S., Peng, K., Shane, B., and Appling, D. R. (2003) J. Biol. Chem. 278, 43178-43187) is responsible for the synthetase activity. The lack of NADP-dependent dehydrogenase activity suggests that this RNA may encode a monofunctional synthetase. Moreover, examination of the primary structure of this novel protein revealed mutations in key residues required for dehydrogenase and cyclohydrolase activities. This monofunctional synthetase completes the pathway for the production of formate from formyltetrahydrofolate in the mitochondria in our model of mammalian one-carbon folate metabolism in embryonic and transformed cells.


Subject(s)
Embryo, Mammalian/cytology , Fibroblasts/cytology , Formate-Tetrahydrofolate Ligase/genetics , Formate-Tetrahydrofolate Ligase/physiology , Methylenetetrahydrofolate Dehydrogenase (NADP)/physiology , Mitochondria/enzymology , Stem Cells/cytology , Amino Acid Sequence , Animals , Blotting, Northern , Cell Line , Cell Line, Transformed , DNA, Complementary/metabolism , Databases as Topic , Exons , Fibroblasts/metabolism , Genotype , Heterozygote , Homozygote , Humans , Methenyltetrahydrofolate Cyclohydrolase/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Mice , Mice, Knockout , Mice, Transgenic , Mitochondria/metabolism , Models, Biological , Models, Genetic , Molecular Sequence Data , Mutation , RNA/chemistry , Sequence Homology, Amino Acid , Software , Time Factors
19.
Biochem Biophys Res Commun ; 315(1): 204-11, 2004 Feb 27.
Article in English | MEDLINE | ID: mdl-15013446

ABSTRACT

To seek the genes involved in the development of colorectal cancer, we analyzed the microarray gene expression profiles of human normal and cancerous colon tissues using the BioExpress database platform. Through the analysis we found one gene named DKFZp586G1517 that was upregulated in colon adenocarcinomas. The full-length cDNA of the DKFZp586G1517 cloned by polymerase chain reaction (PCR) encodes a protein with 978 amino acids, which is homologous to the human cytosolic C(1)-tetrahydrofolate synthetase and contains a mitochondrial target signal at N-terminus. The gene product expressed in 293 cells was localized in mitochondria and processed at the predicted signal cleavage site, supporting the idea that DKFZp586G1517 is a novel mitochondrial C(1)-tetrahydrofolate synthetase (mtC(1)-THFS). The overexpression of mtC(1)-THFS in 293 cells stimulated the colony formation. These results suggest that mtC(1)-THFS may participate in the progression of colorectal cancer by conferring growth advantage and could be a new molecular target for cancer therapy.


Subject(s)
Adenocarcinoma/enzymology , Aminohydrolases/biosynthesis , Colonic Neoplasms/enzymology , Formate-Tetrahydrofolate Ligase/biosynthesis , Methylenetetrahydrofolate Dehydrogenase (NADP)/biosynthesis , Mitochondria/enzymology , Multienzyme Complexes/biosynthesis , Amino Acid Sequence , Aminohydrolases/chemistry , Aminohydrolases/genetics , Cell Division/genetics , Cell Line , Cloning, Molecular , DNA, Complementary/genetics , Formate-Tetrahydrofolate Ligase/chemistry , Formate-Tetrahydrofolate Ligase/genetics , Gene Expression Profiling , Humans , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Molecular Sequence Data , Multienzyme Complexes/chemistry , Multienzyme Complexes/genetics , Protein Structure, Tertiary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Transfection , Up-Regulation
20.
J Biol Chem ; 278(44): 43178-43187, 2003 Oct 31.
Article in English | MEDLINE | ID: mdl-12937168

ABSTRACT

C1-tetrahydrofolate (THF) synthase is a trifunctional enzyme found in eukaryotes that contains the activities 10-formyl-THF synthetase, 5,10-methenyl-THF cyclohydrolase, and 5,10-methylene-THF dehydrogenase. The cytoplasmic isozyme of C1-THF synthase is well characterized in a number of mammals, including humans; but a mitochondrial isozyme has been previously identified only in the yeast Saccharomyces. Here, we report the identification and characterization of the human gene encoding a functional mitochondrial C1-THF synthase. The gene spans 236 kilobase pairs on chromosome 6 and consists of 28 exons plus one alternative exon. The gene encodes a protein of 978 amino acids, including an N-terminal mitochondrial targeting sequence. The mitochondrial isozyme is 61% identical to the human cytoplasmic isozyme. Expression of the gene was detected in most human tissues, but transcripts were highest in placenta, thymus, and brain. Two mRNAs were detected, a 3.6-kb transcript and a 1.1-kb transcript, and both transcripts were observed in varying ratios in each tissue. The shorter transcript results from an alternative splicing event, where exon 7 is spliced to exon 8a instead of exon 8. Exon 8a is derived from an exonized Alu sequence, sharing no homology with exon 8 of the long transcript, and encodes just 15 amino acids followed by a stop codon and a polyadenylation signal. This short transcript potentially encodes a bifunctional enzyme lacking 10-formyl-THF synthetase activity. Both transcripts initiate at the same 5'-site, 107 nucleotides up-stream of the ATG start codon. The full-length (2934 bp) cDNA fused to a C-terminal V5 epitope tag was expressed in Chinese hamster ovary cells. Immunoblots of subfractionated cells revealed a 107-kDa protein only in the mitochondrial fractions of these cells, confirming the mitochondrial localization of the protein. Yeast cells expressing the full-length human cDNA exhibited elevated 10-formyl-THF synthetase activity, confirming its identification as the human mitochondrial C1-THF synthase.


Subject(s)
Aminohydrolases/biosynthesis , Aminohydrolases/genetics , Formate-Tetrahydrofolate Ligase/biosynthesis , Formate-Tetrahydrofolate Ligase/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/biosynthesis , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Mitochondria/enzymology , Multienzyme Complexes/biosynthesis , Multienzyme Complexes/genetics , Alternative Splicing , Amino Acid Sequence , Aminohydrolases/chemistry , Animals , Blotting, Northern , CHO Cells , Chromosomes, Human, Pair 6 , Cloning, Molecular , Codon, Initiator , Codon, Terminator , Cricetinae , Cytoplasm/enzymology , Cytoplasm/metabolism , DNA, Complementary/metabolism , Epitopes , Exons , Formate-Tetrahydrofolate Ligase/chemistry , Humans , Immunoblotting , Introns , Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry , Mitochondria/metabolism , Models, Biological , Models, Genetic , Molecular Sequence Data , Multienzyme Complexes/chemistry , Protein Isoforms , Protein Structure, Tertiary , RNA, Messenger/metabolism , Sequence Homology, Amino Acid , Subcellular Fractions/metabolism , Tissue Distribution , Transfection
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