Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from <i>Thermus thermophilus</i>

Jia, Yunhua; Tanaka, Takeo; Yamauchi, Kazuma; Nishiyama, Makoto; Palmer, David R. J.

doi:10.1042/bj20051711

Cited by 18 publications

(24 citation statements)

References 47 publications

(63 reference statements)

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“…Some organisms such as bacteria and plants use the so-called diaminopimelic acid pathway for biosynthesis of this amino acid. However, other organisms including filamentous fungi, yeast, some Euglena species (Bhattacharjee, 1985) and the bacteria Thermus thermophilus and Pyrococcus horikoshii (Kosuge & Hoshino, 1998;Kobashi et al, 1999;Jia et al, 2006) use the so-called a-aminoadipate pathway (Zabriskie & Jackson, 2000;Xu et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

et al. 2009

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The lysine biosynthetic pathway has to supply large amounts of α-aminoadipic acid for penicillin biosynthesis in Penicillium chrysogenum. In this study, we have characterized the P. chrysogenum L2 mutant, a lysine auxotroph that shows highly increased expression of several lysine biosynthesis genes (lys1, lys2, lys3, lys7). The L2 mutant was found to be deficient in homoaconitase activity since it was complemented by the Aspergillus nidulans lysF gene. We have cloned a gene (named lys3) that complements the L2 mutation by transformation with a P. chrysogenum genomic library, constructed in an autonomous replicating plasmid. The lys3-encoded protein showed high identity to homoaconitases. In addition, we cloned the mutant lys3 allele from the L2 strain that showed a G1534 to A1534 point mutation resulting in a Gly495 to Asp495 substitution. This mutation is located in a highly conserved region adjacent to two of the three cysteine residues that act as ligands to bind the iron–sulfur cluster required for homoaconitase activity. The L2 mutant accumulates homocitrate. Deletion of the lys1 gene (homocitrate synthase) in the L2 strain prevented homocitrate accumulation and reverted expression levels of the four lysine biosynthesis genes tested to those of the parental prototrophic strain. Homocitrate accumulation seems to act as a sensor of lysine-pathway distress, triggering overexpression of four of the lysine biosynthesis genes.

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Section: Introductionmentioning

confidence: 99%

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

et al. 2009

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“…The rate of M. jannaschii HACN-catalyzed cis-homoaconitate hydration is similar to the rate for the T. thermophilus HACN, which has a similar turnover (1.3 s Ϫ1 ) but a lower K m (8.2 M) (15). Furthermore, the M. jannaschii HACN uses cishomoaconitate analogs with two to five methylene groups in the ␥-carboxylate chain, all with similar specificity constants.…”

Section: Discussionmentioning

confidence: 60%

“…Coupled Assay of Hydratase Activity-The hydration of unsaturated intermediates in the forward direction was measured by a coupled reaction with HICDH by monitoring the reduction of NAD ϩ to NADH at 340 nm (15). Reaction mixtures containing 50 mM TAPS-KOH (pH 8.5), 50 mM KCl, 5 mM MgCl 2 , 20 mM ␤-mercaptoethanol, 1 mM NAD ϩ , and 30 g ml Ϫ1 HICDH were degassed as described above, after which MJ1003/MJ1271 holoenzyme was added to a final concentration of 10 g ml Ϫ1 .…”

Section: Methodsmentioning

confidence: 99%

“…The HACN enzyme in CoB biosynthesis has not yet been identified. It is predicted to differ from the previously characterized HACN enzymes that function in ␣-aminoadipate pathways for lysine biosynthesis in Saccharomyces cerevisiae (13), Aspergillus nidulans (14), and the bacterium Thermus thermophilus (15). Along with the homologous 2-methyl-cis-aconitate hydratase and dimethylmalate dehydratase proteins, those HACN proteins catalyze only half of an aconitase-like reaction (16,17).…”

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confidence: 99%

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Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis

Drevland

Jia

Palmer

et al. 2008

Journal of Biological Chemistry

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Homoaconitase enzymes catalyze hydrolyase reactions in the ␣-aminoadipate pathway for lysine biosynthesis or the 2-oxosuberate pathway for methanogenic coenzyme B biosynthesis. Despite the homology of this iron-sulfur protein to aconitase, previously studied homoaconitases catalyze only the hydration of cis-homoaconitate to form homoisocitrate rather than the complete isomerization of homocitrate to homoisocitrate. The MJ1003 and MJ1271 proteins from the methanogen Methanocaldococcus jannaschii formed the first homoaconitase shown to catalyze both the dehydration of (R)-homocitrate to form cishomoaconitate, and its hydration is shown to produce homoisocitrate. This heterotetrameric enzyme also used the analogous longer chain substrates cis-(homo) 2 aconitate, cis-(homo) 3 aconitate, and cis-(homo) 4 aconitate, all with similar specificities. A combination of the homoaconitase with the M. jannaschii homoisocitrate dehydrogenase catalyzed all of the isomerization and oxidative decarboxylation reactions required to form 2-oxoadipate, 2-oxopimelate, and 2-oxosuberate, completing three iterations of the 2-oxoacid elongation pathway. Methanogenic archaeal homoaconitases and fungal homoaconitases evolved in parallel in the aconitase superfamily. The archaeal homoaconitases share a common ancestor with isopropylmalate isomerases, and both enzymes catalyzed the hydration of the minimal substrate maleate to form D-malate. The variation in substrate specificity among these enzymes correlated with the amino acid sequences of a flexible loop in the small subunits.

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“…3H). We hypothesized that the main reason for this is that bound Fe(III) is easily lost from the active center, similar to the [4Fe-4S] cluster in known aconitase enzymes (26,27,32). All amino acid residues of AcnX Type I (possibly) related to Fe(III) binding, substrate recognition, and/or structural folding are completely conserved in AcnX Type IIa , except for a serine residue at the position corresponding to Cys68 of PaAcnX (Fig.…”

Section: R Ni Tvf Ad Gevdr Spc Gs Gt Sar Ia L R Nv Vif Ad Gevdr Spc Gmentioning

confidence: 99%

Characterization of a Novel cis -3-Hydroxy- l -Proline Dehydratase and a trans -3-Hydroxy- l -Proline Dehydratase from Bacteria

et al. 2017

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Hydroxyprolines, such as trans-4-hydroxy-L-proline (T4LHyp), trans-3-hydroxy-L-proline (T3LHyp), and cis-3-hydroxy-L-proline (C3LHyp), are present in some proteins including collagen, plant cell wall, and several peptide antibiotics. In bacteria, genes involved in the degradation of hydroxyproline are often clustered on the genome (L-Hyp gene cluster). We recently reported that an aconitase X (AcnX)-like hypI gene from an L-Hyp gene cluster functions as a monomeric C3LHyp dehydratase (AcnX Type I ). However, the physiological role of C3LHyp dehydratase remained unclear. We here demonstrate that Azospirillum brasilense NBRC 102289, an aerobic nitrogen-fixing bacterium, robustly grows using not only T4LHyp and T3LHyp but also C3LHyp as the sole carbon source. The small and large subunits of the hypI gene (hypI S and hypI L , respectively) from A. brasilense NBRC 102289 are located separately from the L-Hyp gene cluster and encode a C3LHyp dehydratase with a novel heterodimeric structure (AcnX Type IIa ). A strain disrupted in the hypI S gene did not grow on C3LHyp, suggesting its involvement in C3LHyp metabolism. Furthermore, C3LHyp induced transcription of not only the hypI genes but also the hypK gene encoding Δ 1 -pyrroline-2-carboxylate reductase, which is involved in T3LHyp, D-proline, and D-lysine metabolism. On the other hand, the L-Hyp gene cluster of some other bacteria contained not only the AcnX Type IIa gene but also two putative proline racemase-like genes (hypA1 and hypA2). Despite having the same active sites (a pair of Cys/Cys) as hydroxyproline 2-epimerase, which is involved in the metabolism of T4LHyp, the dominant reaction by HypA2 was clearly the dehydration of T3LHyp, a novel type of T3LHyp dehydratase that differed from the known enzyme (Cys/Thr). L-hydroxyproline) degradation in aerobic bacteria, its genetic and molecular information has only recently been elucidated. L-Hydroxyproline metabolic genes are often clustered on bacterial genomes. These loci frequently contain a hypothetical gene(s), whose novel enzyme functions are related to the metabolism of trans-3-hydroxyL-proline and/or cis-3-hydroxyL-proline, a relatively rare L-hydroxyproline in nature. Several L-hydroxyproline metabolic enzymes show no sequential similarities, suggesting their emergence by convergent evolution. Furthermore, transcriptional regulation by trans-4-hydroxy-L-proline, trans-3-hydroxy-L-proline, and/or cis-3-hydroxy-L-proline significantly differs between bacteria. The results of the present study show that several L-hydroxyprolines are available for bacteria as carbon and energy sources and may contribute to the discovery of potential metabolic pathways of another hydroxyproline(s). IMPORTANCE More than 50 years after the discovery of trans-4-hydroxy-L-proline (generally calledKEYWORDS aconitase X, proline racemase superfamily, gene cluster, hydroxyproline, convergent evolution

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Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus

Cited by 18 publications

References 47 publications

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

Transcriptional upregulation of four genes of the lysine biosynthetic pathway by homocitrate accumulation in Penicillium chrysogenum: homocitrate as a sensor of lysine-pathway distress

Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis

Characterization of a Novel cis -3-Hydroxy- l -Proline Dehydratase and a trans -3-Hydroxy- l -Proline Dehydratase from Bacteria

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