An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism

Makino, Yuki; Sato, Takaaki; Kawamura, Hiroki; Hachisuka, Shin-ichi; Takeno, Ryo; Imanaka, Tadayuki; Atomi, Haruyuki

doi:10.1038/ncomms13446

Cited by 30 publications

(31 citation statements)

References 48 publications

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“…The SbnI structure revealed striking structural homology to a recently characterized free serine kinase, SerK, from the archaea Thermococcus kodakarensis (31). SerK can phosphorylate free L-serine using ADP to generate OPS for cysteine biosynthesis (32). Herein, we demonstrate that SbnI is also a free serine kinase that uses ATP to phosphorylate L-serine to yield OPS and ADP (Fig.…”

mentioning

confidence: 61%

“…This fold has been described in a functionally diverse ParB/Srx superfamily of proteins. Members are found in varied biological contexts and thus far are described to bind a nucleotide for kinase, ATPase, or DNase activity (32,36). To our knowledge, no ParB/Srx family member has been found to be directly involved in siderophore biosynthesis.…”

Section: Structure Determination Of Sbnimentioning

confidence: 99%

“…The comparatively low k cat /K m could relate to the physiological role of SbnI in S. aureus. SerK supplies cysteine synthase with OPS to produce cysteine and may represent an ancient heterotrophic mechanism of amino acid metabolism (32). Interestingly, this cysteine synthase is a distant SbnA homolog and a true OPS sulfhydrylase.…”

Section: Sbni Serine Kinase Activity and Role In Sb Biosynthesismentioning

confidence: 99%

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SbnI is a free serine kinase that generates -phospho-l-serine for staphyloferrin B biosynthesis in

Verstraete

Perez-Borrajero

Brown

et al. 2018

Journal of Biological Chemistry

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Staphyloferrin B (SB) is an iron-chelating siderophore produced by in invasive infections. Proteins for SB biosynthesis and export are encoded by the gene cluster, in which SbnI, a member of the ParB/Srx superfamily, acts as a heme-dependent transcriptional regulator of the locus. However, no structural or functional information about SbnI is available. Here, a crystal structure of SbnI revealed striking structural similarity to an ADP-dependent free serine kinase, SerK, from the archaea We found that features of the active sites are conserved, and biochemical assays and P NMR and HPLC analyses indicated that SbnI is also a free serine kinase but uses ATP rather than ADP as phosphate donor to generate the SB precursor-phospho-l-serine (OPS). SbnI consists of two domains, and elevated -factors in domain II were consistent with the open-close reaction mechanism previously reported for SerK. Mutagenesis of Glu and Asp in SbnI disclosed that they are required for kinase activity. The only known OPS source in bacteria is through the phosphoserine aminotransferase activity of SerC within the serine biosynthesis pathway, and we demonstrate that an mutant is a serine auxotroph, consistent with a function in l-serine biosynthesis. However, the mutant strain could produce SB when provided l-serine, suggesting that SbnI produces OPS for SB biosynthesis These findings indicate that besides transcriptionally regulating the locus, SbnI also has an enzymatic role in the SB biosynthetic pathway.

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confidence: 61%

Section: Structure Determination Of Sbnimentioning

confidence: 99%

Section: Sbni Serine Kinase Activity and Role In Sb Biosynthesismentioning

confidence: 99%

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SbnI is a free serine kinase that generates -phospho-l-serine for staphyloferrin B biosynthesis in

Verstraete

Perez-Borrajero

Brown

et al. 2018

Journal of Biological Chemistry

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“…Evolution of the ability to synthesize primary metabolites such as amino acids is among the most important events in the history of life because of its basal and crucial functions in every organism. In the case of prokaryotes, at least two serine biosynthetic pathways are known . In the non‐phosphorylated pathway, serine is synthesized from glycine and 5,10‐methylenetetrahydrofolate by serine hydroxymethyltransferase (SHMT, http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/1/2/1.html).…”

Section: Introductionmentioning

confidence: 99%

Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus

et al. 2018

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Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from phosphoserine via a reaction catalyzed by phosphoserine phosphatase (PSP). Two types of PSP, belonging to distinct protein superfamilies, have been reported. Genomic analyses have revealed that the thermophilic bacterium Thermus thermophilus lacks both homologs while still having the ability to synthesize serine. Here, we purified a protein from T. thermophilus which we biochemically identified as a PSP. A knockout mutant of the responsible gene (TT_C1695) was constructed, which showed serine auxotrophy. These results indicated the involvement of this gene in serine biosynthesis in T. thermophilus. TT_C1695 was originally annotated as a protein with unknown function belonging to the haloacid dehalogenase‐like hydrolase (HAD) superfamily. The HAD superfamily, which comprises phosphatases against a variety of substrates, includes also the classical PSP as a member. However, the amino acid sequence of the TT_C1695 was more similar to phosphatases acting on non‐phosphoserine substrates than classical PSP; therefore, a BLASTP search and phylogenetic analysis failed to predict TT_C1695 as a PSP. Our results strongly suggest that the T. thermophilus PSP and classical PSP evolved specificity for phosphoserine independently. Enzymes Phosphoserine phosphatase (PSP; http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/1/3/3.html); serine hydroxymethyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/1/2/1.html); 3‐phosphoglycerate dehydrogenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/1/1/95.html); 3‐phosphoserine aminotransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/52.html).

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“…The complete genome sequences of these organisms have been determined (26)(27)(28), and gene manipulation systems have been established for T. kodakarensis (29)(30)(31)(32)(33) and T. maritima (34). We have been examining the metabolism of T. kodakarensis in detail and have identified a number of enzymes and pathways that differ from the conventional pathways identified in bacteria and eukaryotes (35)(36)(37). Glycolysis in this archaeon is brought about by a modified Embden-Meyerhof pathway, which is found in members of the Thermococcales (38).…”

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confidence: 99%

An In Vitro Enzyme System for the Production of myo -Inositol from Starch

Fujisawa

Fujinaga

Atomi

2017

Appl Environ Microbiol

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We developed an in vitro enzyme system to produce myo-inositol from starch. Four enzymes were used, maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase (MIPS), and inositol monophosphatase (IMPase). The enzymes were thermostable: MalP and PGM from the hyperthermophilic archaeon Thermococcus kodakarensis, MIPS from the hyperthermophilic archaeon Archaeoglobus fulgidus, and IMPase from the hyperthermophilic bacterium Thermotoga maritima. The enzymes were individually produced in Escherichia coli and partially purified by subjecting cell extracts to heat treatment and removing denatured proteins. The four enzyme samples were incubated at 90°C with amylose, phosphate, and NAD ϩ , resulting in the production of myo-inositol with a yield of over 90% at 2 h. The effects of varying the concentrations of reaction components were examined. When the system volume was increased and NAD ϩ was added every 2 h, we observed the production of 2.9 g myo-inositol from 2.9 g amylose after 7 h, achieving gram-scale production with a molar conversion of approximately 96%. We further integrated the pullulanase from T. maritima into the system and observed myo-inositol production from soluble starch and raw potato with yields of 73% and 57 to 61%, respectively. IMPORTANCE myo-Inositol is an important nutrient for human health and provides a wide variety of benefits as a dietary supplement. This study demonstrates an alternative method to produce myo-inositol from starch with an in vitro enzyme system using thermostable maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase, and myo-inositol monophosphatase. By utilizing MalP and PGM to generate glucose 6-phosphate, we can avoid the addition of phosphate donors such as ATP, the use of which would not be practical for scaled-up production of myo-inositol. myo-Inositol was produced from amylose on the gram scale with yields exceeding 90%. Conversion rates were also high, producing over 2 g of myo-inositol within 4 h in a 200-ml reaction mixture. By adding a thermostable pullulanase, we produced myo-inositol from raw potato with yields of 57 to 61% (wt/wt). The system developed here should provide an attractive alternative to conventional methods that rely on extraction or microbial production of myo-inositol.

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An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism

Cited by 30 publications

References 48 publications

SbnI is a free serine kinase that generates -phospho-l-serine for staphyloferrin B biosynthesis in

SbnI is a free serine kinase that generates -phospho-l-serine for staphyloferrin B biosynthesis in

Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus

An In Vitro Enzyme System for the Production of myo -Inositol from Starch

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