Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes

Abstract

Proteins of unknown function belonging to cog1816 and cog0402 were characterized. Sav2595 from Steptomyces avermitilis MA-4680, Acel0264 from Acidothermus cellulolyticus 11B, Nis0429 from Nitratiruptor sp. SB155-2 and Dr0824 from Deinococcus radiodurans R1 were cloned, purified, and their substrate profiles determined. These enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. It was shown here that these enzymes actually deaminate 6-aminodeoxyfutalosine. The deamination of 6-aminodeoxyfutalosine is part of an alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminodeoxyfutalosine is deaminated by these enzymes with catalytic efficiencies greater than 105 M−1 s−1, Km values of 0.9 to 6.0 μM and kcat values of 1.2 to 8.6 s−1. Adenosine, 2′-deoxyadenosine, thiomethyladenosine, and S-adenosylhomocysteine are deaminated at least an order of magnitude slower than 6-aminodeoxyfutalosine. The crystal structure of Nis0429 was determined and the substrate, 6-aminodeoxyfutalosine, was positioned in the active site, based on the presence of adventitiously bound benzoic acid. In this model Ser-145 interacts with the carboxylate moiety of the substrate. The structure of Dr0824 was also determined, but a collapsed active site pocket prevented docking of substrates. A computational model of Sav2595 was built based on the crystal structure of adenosine deaminase and substrates were docked. The model predicted a conserved arginine after β-strand 1 to be partially responsible for the substrate specificity of Sav2595.

Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori

“…Both Fe 2+ and Zn 2+ were modeled and refined on the basis of the coordination geometry and refinement parameters. The precedent of the Fe 2+ and Zn 2+ atoms was established in the original description of the closely related enzyme (Hp0267, 96% identical) from H. pylori 26695 and reported to contain both Fe 2+ and Zn 2+ by direct metal analysis and by metal substitution experiments. ,, …”

“…The precedent of the Fe 2+ and Zn 2+ atoms was established in the original description of the closely related enzyme (Hp0267, 96% identical) from H. pylori 26695 and reported to contain both Fe 2+ and Zn 2+ by direct metal analysis and by metal substitution experiments. 22,39,42 Most adenosine deaminases (both eukaryotes and prokaryotes) use Zn 2+ as the metal cofactor. 43−45 The metal content of HpAFLDA was quantified for both Fe 2+ and Zn 2+ content (Supporting Information).…”

“…Deamination activity on AFL has been reported in Sav2595 from Steptomyces avermitilis as well as its distantly related orthologs (Acel0264, Dr0824, and Nis0429) from three thermophilic bacteria . The characterized catalytic efficiencies for AFL deamination range from 4.8 × 10 6 to 7.9 × 10 5 M –1 s –1 , which are approximately 1–2 orders of magnitude higher than that for jhp0252.…”

Revisiting the methionine salvage pathway and its paralogues

“…It appears that, because MTA displays a reactive group smaller than that of futalosine, the MSP may have been recruited from an alternative pathway of menaquinone biosynthesis. In line with this view, a futalosinebased menaquinone pathway exists also with adenine instead of hypoxanthine as the start point nucleoside (Arakawa et al, 2011;Goble et al, 2013). At least three different futalosine-related pathways exist in bacteria, which make it difficult to infer reliable origins for the fate of these nucleosides (Zhi et al, 2014).…”

Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tü 365

“…Bioinformatical analysis searching for MqnA, revealed the presence of a gene cluster probably encoding menaquinone biosynthesis in S. collinus Tü 365, since it exhibits high similarity to the menaquinone biosynthesis genes of S. coelicolor (Table 8). However, in contrast to S. coelicolor, where the mqn genes were found to be scattered across the genome [16], in S. collinus Tü 365 most genes are clustered with exception of mqnB and mqnD orthologs.…”