Chemistry of enediynyl azides: activation through a novel pathway

The spontaneous activation of a nonaromatic enediynyl azide under ambient conditions has been demonstrated. The aromatic enediyne followed the expected cycloaddition with the alkene in the neighbouring arm to form a stable bridged bicyclic enediyne

Anaerobic biosynthesis of the lower ligand of vitamin B12

Vitamin B(12) (cobalamin) is required by humans and other organisms for diverse metabolic processes, although only a subset of prokaryotes is capable of synthesizing B(12) and other cobamide cofactors. The complete aerobic and anaerobic pathways for the de novo biosynthesis of B(12) are known, with the exception of the steps leading to the anaerobic biosynthesis of the lower ligand, 5,6-dimethylbenzimidazole (DMB). Here, we report the identification and characterization of the complete pathway for anaerobic DMB biosynthesis. This pathway, identified in the obligate anaerobic bacterium Eubacterium limosum, is composed of five previously uncharacterized genes, bzaABCDE, that together direct DMB production when expressed in anaerobically cultured Escherichia coli. Expression of different combinations of the bza genes revealed that 5-hydroxybenzimidazole, 5-methoxybenzimidazole, and 5-methoxy-6-methylbenzimidazole, all of which are lower ligands of cobamides produced by other organisms, are intermediates in the pathway. The bza gene content of several bacterial and archaeal genomes is consistent with experimentally determined structures of the benzimidazoles produced by these organisms, indicating that these genes can be used to predict cobamide structure. The identification of the bza genes thus represents the last remaining unknown component of the biosynthetic pathway for not only B(12) itself, but also for three other cobamide lower ligands whose biosynthesis was previously unknown. Given the importance of cobamides in environmental, industrial, and human-associated microbial metabolism, the ability to predict cobamide structure may lead to an improved ability to understand and manipulate microbial metabolism

Exploring Prokaryotic Thiamin Biosynthesis: Mechanistic Studies On Thiamin Thiazole Synthase And Pyrimidine Synthase

Thiamin (Vitamin B1) is made from a coupling a thiazole and a pyrimidine unit, which are assembled separately. Studies have shown that the biosyntheses of thiazole and pyrimidine are different in prokaryotes versus eukaryotes. Understanding of thiamin biosynthesis is still incomplete and a lot of new discoveries relating to the enzymes in its biosynthesis have been explored in depth revealing new mechanisms and enzymology. In prokaryotes, five different enzymes are known to be directly involved in thiamin thiazole biosynthesis. The in vitro reconstitution of this enzymatic pathway has been achieved and detailed insights have been obtained, however, the very small quantity of product produced in this in vitro reconstitution prevented direct characterization of its structure. We were able to study the last few steps on the prokaryotic thiamin thiazole pathway in greater detail, and elucidate the structure of the final product of the thiazole synthase to be the thiazole tautomer phosphate. We were also able to assign function to a gene involved in aromatization of the unstable thiazole tautomer phosphate to the thiazole carboxylate phosphate. We also knew that a single gene product ThiC converts amino-imidazole ribonucleotide, an intermediate in the purine nucleotide biosynthesis, to HMP, using a complex rearrangement reaction. This enzyme had been very difficult to isolate and study biochemically because it was air-sensitive and its cofactors were unknown. We recently were able to show that it was a [4Fe-4S] cluster containing enzyme, and belonged to the radical SAM family. The 4Fe-4S cluster binding motif (CX2-CX4-C) of ThiC is different from the motif (CX3-CX2-C) conventionally used by the other established members of this family. With the pure protein with a well-reconstituted Fe-S cluster, we were able to achieve remarkable enhancement in activity in vitro, in a defined biochemical system. True products of this reaction were thus identified to be HMP-phosphate and 5'-deoxyadenosine. We were also able to establish the fate of all the C atoms of the substrate, and have other insights into the mechanism of this complex enzyme with regard to the unprecedented rearrangement it brings about. Further mechanistic characterization of the remarkable rearrangement reaction catalyzed by ThiC is in progress

Unique Biochemical and Sequence Features Enable BluB To Destroy Flavin and Distinguish BluB from the Flavin Monooxygenase Superfamily

Vitamin B12 (cobalamin) is an essential micronutrient for humans that is synthesized by only a subset of bacteria and archaea. The aerobic biosynthesis of 5,6-dimethylbenzimidazole, the lower axial ligand of cobalamin, is catalyzed by the "flavin destructase" enzyme BluB, which fragments reduced flavin mononucleotide following its reaction with oxygen to yield this ligand. BluB is similar in sequence and structure to members of the flavin oxidoreductase superfamily, yet the flavin destruction process has remained elusive. Using stopped-flow spectrophotometry, we find that the flavin destructase reaction of BluB from Sinorhizobium meliloti is initiated with canonical flavin-O2 chemistry. A C4a-peroxyflavin intermediate is rapidly formed in BluB upon reaction with O2, and has properties similar to those of flavin-dependent hydroxylases. Analysis of reaction mixtures containing flavin analogues indicates that both formation of the C4a-peroxyflavin and the subsequent destruction of the flavin to form 5,6-dimethylbenzimidazole are influenced by the electronic properties of the flavin isoalloxazine ring. The flavin destruction phase of the reaction, which results from the decay of the C4a-peroxyflavin intermediate, occurs more efficiently at pH >7.5. Furthermore, the BluB mutants D32N and S167G are specifically impaired in the flavin destruction phase of the reaction; nevertheless, both form the C4a-peroxyflavin nearly quantitatively. Coupled with a phylogenetic analysis of BluB and related flavin-dependent enzymes, these results demonstrate that the BluB flavin destructase family can be identified by the presence of active site residues D32 and S167

Functional annotation of putative fadE9 of Mycobacterium tuberculosis as isobutyryl-CoA dehydrogenase involved in valine catabolism

Members of the Acyl-CoA dehydrogenase (ACADs) family of enzymes play a crucial role in cholesterol and steroid catabolism and are widely studied in the oldest known human pathogen, Mycobacterium tuberculosis (Mtb). However, there is a paucity of information on ACADs involved in branched chain amino acid catabolism. Here we characterized one of the putative ACAD enzyme, fadE9, as ``Isobutyryl CoA Dehydrogenase (IBDH)'' using a combined computational and experimental approach, guided by homology modeled structural information, affirming its role in valine catabolism. Multiple sequence alignment and phylogenetic analysis place it in a separate cluster from a recently identified family of alpha(2)beta(2)-heterotetramer ACADs in Mtb, based on the position of the conserved Arg247 and catalytic Glu368 residues. The conserved Arg247 was predicted to play an essential role at the center of H-bonding network of reaction center and was confirmed by the reduced activity of R247K mutant Thus, in addition to the finding of an architecturally distinct alpha(2)beta(2)-heterotetramer among ACADs, these studies also highlight the differences between MtIBDH, fadE9 from the other ACADs that are involved in cholesterol and steroid catabolism of Mtb. (C) 2018 Published by Elsevier B.V

Unique Biochemical and Sequence Features Enable BluB To Destroy Flavin and Distinguish BluB from the Flavin Monooxygenase Superfamily

Vitamin B₁₂ (cobalamin) is an essential micronutrient for humans that is synthesized by only a subset of bacteria and archaea. The aerobic biosynthesis of 5,6-dimethylbenzimidazole, the lower axial ligand of cobalamin, is catalyzed by the “flavin destructase” enzyme BluB, which fragments reduced flavin mononucleotide following its reaction with oxygen to yield this ligand. BluB is similar in sequence and structure to members of the flavin oxidoreductase superfamily, yet the flavin destruction process has remained elusive. Using stopped-flow spectrophotometry, we find that the flavin destructase reaction of BluB from <i>Sinorhizobium meliloti</i> is initiated with canonical flavin–O₂ chemistry. A C4a-peroxyflavin intermediate is rapidly formed in BluB upon reaction with O₂, and has properties similar to those of flavin-dependent hydroxylases. Analysis of reaction mixtures containing flavin analogues indicates that both formation of the C4a-peroxyflavin and the subsequent destruction of the flavin to form 5,6-dimethylbenzimidazole are influenced by the electronic properties of the flavin isoalloxazine ring. The flavin destruction phase of the reaction, which results from the decay of the C4a-peroxyflavin intermediate, occurs more efficiently at pH >7.5. Furthermore, the BluB mutants D32N and S167G are specifically impaired in the flavin destruction phase of the reaction; nevertheless, both form the C4a-peroxyflavin nearly quantitatively. Coupled with a phylogenetic analysis of BluB and related flavin-dependent enzymes, these results demonstrate that the BluB flavin destructase family can be identified by the presence of active site residues D32 and S167

Cobamide Structure Depends on Both Lower Ligand Availability and CobT Substrate Specificity

SummaryCobamides are members of the vitamin B12 family of cofactors that function in a variety of metabolic processes and are synthesized only by prokaryotes. Cobamides produced by different organisms vary in the structure of the lower axial ligand. Here we explore the molecular factors that control specificity in the incorporation of lower ligand bases into cobamides. We find that the cobT gene product, which activates lower ligand bases for attachment, limits the range of lower ligand bases that can be incorporated by bacteria. Furthermore, we demonstrate that the substrate specificity of CobT can be predictably altered by changing two active site residues. These results demonstrate that sequence variations in cobT homologs contribute to cobamide structural diversity. This analysis could open new routes to engineering specific cobamide production and understanding cobamide-dependent processes