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PubMedDate not supplied

A carbon-skeleton walk: a novel double rearrangement of glutaryl-CoA catalyzed by the human methylmalonyl-CoA mutase.

Methylmalonyl-CoA mutase is a member of the coenzyme B12-dependent family of isomerases and interconverts methylmalonyl-CoA and succinyl-CoA. We have examined the ability of the enzyme to effect a double rearrangement reaction when presented with glutaryl-CoA, a substrate analog with a three-carbon template on which two successive 1,2 migrations can occur. Our results demonstrate that the enzyme converts glutaryl-CoA to both methylsuccinyl-CoA and ethylmalonyl-CoA. To our knowledge, this is the first example of a double rearrangement reaction catalyzed by a coenzyme B12-dependent enzyme.

Acyl Coenzyme A↗

PubMed1995

Cobalt-vitamin B12 deficiency and the activity of methylmalonyl CoA mutase and methionine synthase in cattle.

Cobalt deficiency was induced in cattle by feeding two groups of animals either a basal diet that was very low in Co (12.9-17.6 micrograms Co per kg), or the same diet supplemented with cobalt, for a total of 64 weeks. Vitamin B12 deficiency was induced, as judged by hepatic concentrations of vitamin B12 and plasma concentrations of MMA. However, the activity of holo-methylmalonyl CoA mutase was significantly reduced only in brain. This was reflected in very minor alterations in the tissue concentrations of branched chain- and odd numbered-fatty acids. The activity of holo-methionine synthase was significantly reduced in liver and brain, but there were no consequent alterations in the concentrations of phosphatidyl choline and phosphatidyl ethanolamine. This study confirms that cattle are less susceptible to the effects of cobalt deficiency than sheep, and concludes that prolonged cobalt deficiency had little significant effect on tissue metabolism.

5-Methyltetrahydrofolate-Homocysteine S-Methyltran↗

PubMed2001

A protein pre-organized to trap the nucleotide moiety of coenzyme B(12): refined solution structure of the B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum.

Uniformly (13)C,(15)N-labeled MutS, the coenzyme B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum, was prepared by overexpression from an Escherichia coli strain. Multidimensional heteronuclear NMR spectroscopic experiments with aqueous solutions of (13)C,(15)N-labeled MutS provided signal assignments for roughly 90% of the 1025 hydrogen, 651 carbon, and 173 nitrogen atoms and resulted in about 1800 experimental restraints. Based on the information from the NMR experiments, the structure of MutS was calculated, confirming the earlier, less detailed structure obtained with (15)N-labeled MutS. The refined analysis allowed a precise determination of the secondary and tertiary structure including several crucial side chain interactions. The structures of (the apoprotein) MutS in solution and of the B(12)-binding subunit in the crystal of the corresponding homologous holoenzyme from Clostridium cochlearium differ only in a section that forms the well-structured helix alpha1 in the crystal structure and that also comprises the cobalt-coordinating histidine residue. In the apoprotein MutS, this part of the B(12)-binding subunit is dynamic. The carboxy-terminal end of this section is conformationally flexible and has significant propensity for an alpha-helical structure ("nascent helix"). This dynamic section in MutS is a decisive element for the binding of the nucleotide moiety of coenzyme B(12) and appears to be stabilized as a helix (alpha1) upon trapping of the nucleotide of the B(12) cofactor.

Amino Acid Sequence↗

PubMed2006

A new methodology for the synthesis of fluorinated exo-glycals and their time-dependent inhibition of UDP-galactopyranose mutase.

Fluorinated carbohydrates constitute a very important class of mechanistic probes for glycosyl-processing enzymes. In this study, we describe the first synthesis of fluorinated and phosphonylated exo-glycals and their corresponding nucleotide sugars in the galactofuranose series. The synthetic protocol that we have developed is a Selectfluor-mediated fluorination/elimination sequence on phosphonylated exo-glycals, and it offers a new entry into fluorinated carbohydrate chemistry. The challenging E/Z stereochemical assignment of the resulting tetrasubstituted alkenes, which bear an alkoxy, an alkyl, a fluoro, and a phosphonyl group, has been achieved through NMR experiments. The corresponding (E)- and (Z)-nucleotide fluorosugars have been prepared and tested as inhibitors of UDP-galactopyranose mutase (UGM). UGM is a flavoenzyme that catalyzes the isomerization of uridine diphosphate(UDP)-galactopyranose into UDP-galactofuranose, a key step of the biosynthesis of important mycobacterial cell-wall glycoconjugates. The two diastereomeric molecules were found to display time-dependent inactivation of UGM, as expected from preliminary results using non-fluorinated exo-glycal nucleotides. The inhibitory properties of the two fluorinated molecules led us to suggest that the inactivation mechanism proceeds through two-electron processes, despite the presence of the flavin cofactor within the UGM catalytic site.

Fluorine↗

PubMed1984

The stereochemistry of the formation of the methyl group in the glutamate mutase-catalysed reaction in Clostridium tetanomorphum.

The adenosylcobalamin-dependent enzyme glutamate mutase from Clostridium tetanomorphum catalyses the reversible rearrangement of (2S)-glutamate to (2S,3S)-3- methylaspartate . In this conversion 6 carbon centers are involved. The stereochemistry of 4 has been elucidated whereas the formation of the methyl group from the methylene group remains to be established. To solve this problem, (2S,3R)- and (2S,3S)-[3,3-2H1,3H]glutamates were prepared via the 2-oxo[3,3-2H2 or 3H] glutarates by incubation with isocitrate dehydrogenase in deuterium oxide or tritiated water. The labelled glutamates were fermented with growing cells of C. tetanomorphum to butyrate and acetate. Butyrate was further degraded to acetate in which methyl group over 90% of the tritium of the starting glutamate was retained. The chirality of the acetates was determined with malate synthase and fumarase. In both samples complete racemisation was found. This result confirms the rule that racemisation occurs in all adenosylcobalamin-dependent rearrangements in which methyl groups are formed. A methylene radical as intermediate could explain these observations. In a control experiment inversion of configuration in the formation of the methine group of (2S,3S)-3-methylaspartate from the methylene group of (2S)-glutamate was confirmed. Glutamates stereospecifically labelled at C-4 were synthesized from chiral acetates via citrate.

Amino Acid Isomerases↗

PubMed1992

Identification of a paramagnetic species as an early intermediate in the coenzyme B12-dependent glutamate mutase reaction. A cob(II)amide?

Highly active and cobamide-free glutamate mutase was obtained from Clostridium cochlearium by a modification of the original purification procedure. After incubation of the enzyme with dithiothreitol, adenosylcobalamin (coenzyme B12) and the substrate (S)-glutamate, a paramagnetic species was observed by EPR-spectroscopy. The signal was maximal within 15 ms after mixing with glutamate. Different signals were detected after incubating the system with the competitive inhibitors (2S,4S)-4-fluoroglutamate or 2-methyleneglutarate instead of the substrate. The former developed with an at least 100-fold lower rate then the signal with glutamate. All three signals are probably due to low-spin cob(II)amide species with an extraordinary low gxy value as compared with cob(II)alamin.

Amino Acid Isomerases↗

PubMed1993

Cloning and sequencing of glutamate mutase component E from Clostridium tetanomorphum.

The nucleotide sequence of the large subunit E of glutamate mutase of Clostridium tetanomorphum was determined. The protein consists of 483 amino acids and is not made in a precursor form, thus excluding the possibility of subunit E being a pyruvoyl enzyme. It shows no homology to any other protein in the database, and while binding coenzyme B12, a conspicuous B12 binding motif, shared amongst other proteins, is not detectable at the sequence level.

Amino Acid Isomerases↗

PubMed1982

Chorismate mutase-prephenate dehydrogenase from Escherichia coli. Kinetic mechanism of the prephenate dehydrogenase reaction.

The mechanism of the dehydrogenase reaction catalyzed by chorismate mutase-prephenate dehydrogenase (chorismate pyruvatemutase, EC 5.4.99.5-prephenate:NAD+ oxidoreductase (decarboxylating), EC 1.3.1.12) has been investigated using steady-state kinetic techniques. The steady-state velocity pattern in the absence of products as well as product and dead-end inhibition patterns are consistent with a random mechanism in which two dead-end complexes, E-NADH-prephenate and E-NAD-hydroxyphenylpyruvate, are formed, and in which all steps are in rapid equilibrium except that concerned with the interconversion of central ternary complexes. Values have been determined for the maximum velocity of the reaction as well as for the kinetic parameters associated with the combination of substrates, products and the dead-end inhibitor, AMP, with various enzyme forms. The results indicate that when albumin is present in the reaction mixture, the presence of one substrate on the enzyme does not affect the combination of the second substrate. On the other hand, the binding of 4-hydroxyphenylpyruvate is enhanced by the presence of NAD and the binding of NADH is enhanced by the presence of prephenate on the enzyme. These results contrast with the finding that the inhibitory analogue, AMP, binds more strongly to the free enzyme than to the E-prephenate complex.

Adenosine Monophosphate↗

PubMed1982

Production of chorismate mutase-prephenate dehydrogenase by a strain of Escherichia coli carrying a multicopy, tyrA plasmid. Isolation and properties of the enzyme.

A multicopy plasmid that contains the tyrosine operon has been used to transform strains of Escherichia coli K-12. The resultant strains yielded levels of chorismate mutase-prephenate dehydrogenase that were up to 5000-fold higher than that given by the parent strain and about 6-fold higher than that given by a tyrR strain. The production of enzyme fell when tetracycline was omitted from the growth medium because of the loss of the plasmid. The bifunctional enzyme was isolated in good yield by a simple purification procedure and shown to possess properties identical to those exhibited by the enzyme from a tyrR strain.

Escherichia coli↗

PubMed2006

1,4-Anhydrogalactopyranose is not an intermediate of the mutase catalyzed UDP-galactopyranose/furanose interconversion.

UDP-galactopyranose mutase (UGM) catalyzes the isomerization of UDP-galactopyranose (UDP-Galp) into UDP-galactofuranose (UDP-Galf), an essential step of the mycobacterial cell wall biosynthesis. The first mechanistic assumption proposed in the literature was the involvement of 1,4-anhydrogalactose 1 as intermediate of this ring contraction. To confirm or rule out this hypothesis, we synthesized 1 and engaged it in reactions with UGM. The expected formations of UDP-Galf and UDP-Galp were never observed, thus showing that 1 is not, in fact, a low energy intermediate of this enzymatic contraction.

Catalysis↗

PubMed2004

Synthesis of a novel class of sulfonium ions as potential inhibitors of UDP-galactopyranose mutase.

Two sulfonium salts of 1,4-anhydro-4-thio-D-galactitol, with structures related to the known sulfonium salt glycosidase inhibitor, salacinol, have been synthesized as potential inhibitors of UDP-galactopyranose mutase. The synthetic strategy relies on the alkylation reaction of 1,4-anhydro-2,3,5,6-tetra-O-benzyl-4-thio-D-galactitol at the sulfur atom with 2,4-O-benzylidene-D- or -L-erythritol-1,3-cyclic sulfate. In each case, the reaction proceeded stereoselectively to yield only one stereoisomer at the stereogenic sulfur atom. The effect of the polar solvent, 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), in promoting high-yielding reactions is highlighted. The target compounds are then obtained by hydrogenolysis.

Enzyme Inhibitors↗

PubMed2006

Chemical probes of UDP-galactopyranose mutase.

Many pathogenic prokaryotes and eukaryotes possess the machinery required to assemble galactofuranose (Galf)-containing glycoconjugates; these glycoconjugates can be critical for virulence or viability. Accordingly, compounds that block Galf incorporation may serve as therapeutic leads or as probes of the function of Galf-containing glycoconjugates. The enzyme UDP-galactopyranose mutase (UGM) is the only known generator of UDP-galactofuranose, the precursor to Galf residues. We previously employed a high-throughput fluorescence polarization assay to investigate the Klebsiella pneumoniae UGM. We demonstrate the generality of this assay by extending it to UGM from Mycobacterium tuberculosis. To identify factors influencing binding, we synthesized a directed library containing a 5-arylidene-2-thioxo-4-thiazolidinone core, a structure possessing features common to ligands for both homologs. Our studies offer a blueprint for identifying inhibitors of the growing family of UGM homologs and provide insight into UGM inhibition.

Binding Sites↗

PubMed2003

Chromosomal organization and transcription analysis of genes in the vicinity of Pseudomonas aeruginosa glmM gene encoding phosphoglucosamine mutase.

A computer-aided analysis of the Pseudomonas aeruginosa PAO1 genome surrounding the glmM gene was carried out and the organization of this chromosomal region was compared with the equivalent regions in other gamma-proteobacteria species with the genome sequence available. glmM encodes the enzyme phosphoglucosamine mutase which catalyses the interconversion of glucosamine-6-phosphate into glucosamine-1-phosphate in the biosynthetic pathway leading to the synthesis of UDP-N-acetylglucosamine which is simultaneously a precursor for the biosynthesis of cell-wall peptidoglycan and outer membrane lipopolysaccharide. Northern blot analysis suggests that glmM may be a part of the five-cistron operonic structure composed by the Escherichia coli homologues ftsJ, ftsH, folP, glmM, and tpiA. The secG gene, downstream tpiA, does not make part of this polygenic organization, being actively transcribed as a monocistronic mRNA during transition to the stationary phase of growth. Differently, transcription of genes in the glmM operon is more active in the early exponential phase, decreasing with the increase of cell density during exponential growth and reaching negligible values in stationary phase cells.

Blotting, Northern↗

PubMed2001

Chemical synthesis of UDP-beta-L-arabinofuranose and its turnover to UDP-beta-L-arabinopyranose by UDP-galactopyranose mutase.

Uridine-5'-diphospho-beta-L-arabinofuranose, a possible donor of L-arabinofuranose residues in plants, was synthesized. This compound, in the presence of UDP-galactopyranose mutase, underwent interconversion with UDP-beta-L-arabinopyranose that is a likely precursor of L-arabinofuranose in vivo. This result provided a working model for the biogenesis of arabinofuranose in plants.

Chromatography, High Pressure Liquid↗

PubMed1999

Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.

BACKGROUND: Conversion of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxyaminoimidazole ribonucleotide (CAIR) in Escherichia coli requires two proteins - PurK and PurE. PurE has recently been shown to be a mutase that catalyzes the unusual rearrangement of N(5)-carboxyaminoimidazole ribonucleotide (N(5)-CAIR), the PurK reaction product, to CAIR. PurEs from higher eukaryotes are homologous to E. coli PurE, but use AIR and CO(2) as substrates to produce CAIR directly. RESULTS: The 1.50 A crystal structure of PurE reveals an octameric structure with 422 symmetry. A central three-layer (alphabetaalpha) sandwich domain and a kinked C-terminal helix form the folded structure of the monomeric unit. The structure reveals a cleft at the interface of two subunits and near the C-terminal helix of a third subunit. Co-crystallization experiments with CAIR confirm this to be the mononucleotide-binding site. The nucleotide is bound predominantly to one subunit, with conserved residues from a second subunit making up one wall of the cleft. CONCLUSIONS: The crystal structure of PurE reveals a unique quaternary structure that confirms the octameric nature of the enzyme. An analysis of the native crystal structure, in conjunction with sequence alignments and studies of co-crystals of PurE with CAIR, reveals the location of the active site. The environment of the active site and the analysis of conserved residues between the two classes of PurEs suggests a model for the differences in their substrate specificities and the relationship between their mechanisms.

Amino Acid Sequence↗

PubMed2001

Crystal structure of precorrin-8x methyl mutase.

BACKGROUND: The crystal structure of precorrin-8x methyl mutase (CobH), an enzyme of the aerobic pathway to vitamin B12, provides evidence that the mechanism for methyl migration can plausibly be regarded as an allowed [1,5]-sigmatropic shift of a methyl group from C-11 to C-12 at the C ring of precorrin-8x to afford hydrogenobyrinic acid. RESULTS: The dimeric structure of CobH creates a set of shared active sites that readily discriminate between different tautomers of precorrin-8x and select a discrete tautomer for sigmatropic rearrangement. The active site contains a strictly conserved histidine residue close to the site of methyl migration in ring C of the substrate. CONCLUSION: Analysis of the structure with bound product suggests that the [1,5]-sigmatropic shift proceeds by protonation of the ring C nitrogen, leading to subsequent methyl migration.

Amino Acid Sequence↗

PubMed2001

The role of the active site glutamate in the rearrangement of glutamate to 3-methylaspartate catalyzed by adenosylcobalamin-dependent glutamate mutase.

BACKGROUND: Adenosylcobalamin (coenzyme B(12))-dependent enzymes catalyze a variety of chemically difficult reactions that proceed through the generation of free radical intermediates. A long-standing question is how proteins stabilize what are normally regarded as highly reactive organic radicals and direct them towards productive reactions. In glutamate mutase the carboxylate of Glu171 hydrogen bonds with the amino group of the substrate. We have investigated the role of this residue in the enzyme mechanism. RESULTS: Several sterically and functionally conservative mutations were introduced at position 171. In the most impaired mutant, Glu171Gln, k(cat) is reduced 50-fold, although the K(m) for glutamate is little affected. In the wild-type enzyme activity was pH-dependent and the acidic limb of the activity curve titrated with an apparent pK(a) of 6.6 on V(max), whereas for the sluggish Glu171Gln mutant activity is independent of pH. The steady state deuterium kinetic isotope effect is reduced in the mutant enzyme, but the steady state concentration of free radical species on the enzyme (as measured by the steady state concentration of cob(II)alamin) is unaffected by the mutation. CONCLUSIONS: The properties of the mutant proteins are consistent with the hypothesis that Glu171 acts as a general base that serves to deprotonate the amino group of the substrate during catalysis. Deprotonation is expected to facilitate the formation of the glycyl radical intermediate formed during the inter-conversion of substrate and product radicals, but to have little effect on the stability of product or substrate radicals themselves.

Aspartic Acid↗

PubMed2002

Coenzyme B(12) dependent glutamate mutase.

The crystal structure of glutamate mutase with bound coenzyme B(12) suggests a radical shuttling mechanism within the active site of the enzyme. Quantum chemical calculations of the rearrangement in combination with kinetic and mutational studies suggest the catalytic mechanism of this enzyme to proceed via a fragmentation/recombination sequence with intermediates stabilized by partial protonation/deprotonation. Crucial residues in the active site have been identified. Solution structure studies indicate the mechanism of B(12) binding to the apoenzyme.

Binding Sites↗