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  1. Article ; Online: An energy-conserving reaction in amino acid metabolism catalyzed by arginine synthetase.

    Michimori, Yuta / Yokooji, Yuusuke / Atomi, Haruyuki

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 16, Page(s) e2401313121

    Abstract: All forms of life are presumed to synthesize arginine from citrulline via a two-step pathway consisting of argininosuccinate synthetase and argininosuccinate lyase using citrulline, adenosine 5'-triphosphate (ATP), and aspartate as substrates. Conversion ...

    Abstract All forms of life are presumed to synthesize arginine from citrulline via a two-step pathway consisting of argininosuccinate synthetase and argininosuccinate lyase using citrulline, adenosine 5'-triphosphate (ATP), and aspartate as substrates. Conversion of arginine to citrulline predominantly proceeds via hydrolysis. Here, from the hyperthermophilic archaeon
    MeSH term(s) Ligases ; Arginine/metabolism ; Citrulline/metabolism ; Ammonia ; Ornithine/genetics ; Adenosine Triphosphate/metabolism ; Phosphates ; Adenosine ; Catalysis
    Chemical Substances Ligases (EC 6.-) ; Arginine (94ZLA3W45F) ; Citrulline (29VT07BGDA) ; Ammonia (7664-41-7) ; Ornithine (E524N2IXA3) ; Adenosine Triphosphate (8L70Q75FXE) ; Phosphates ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2024-04-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2401313121
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  2. Article: Biochemical and genetic examination of two aminotransferases from the hyperthermophilic archaeon

    Su, Yu / Michimori, Yuta / Atomi, Haruyuki

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1126218

    Abstract: The hyperthermophilic ... ...

    Abstract The hyperthermophilic archaeon
    Language English
    Publishing date 2023-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1126218
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  3. Article ; Online: Development of a rapid and highly accurate method for

    Fukuyama, Yuto / Shimamura, Shigeru / Sakai, Sanae / Michimori, Yuta / Sumida, Tomomi / Chikaraishi, Yoshito / Atomi, Haruyuki / Nunoura, Takuro

    ISME communications

    2024  Volume 4, Issue 1, Page(s) ycad006

    Abstract: Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for ... ...

    Abstract Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 [Formula: see text] 10
    Language English
    Publishing date 2024-01-10
    Publishing country England
    Document type Journal Article
    ISSN 2730-6151
    ISSN (online) 2730-6151
    DOI 10.1093/ismeco/ycad006
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  4. Article ; Online: Microbe Profile:

    Atomi, Haruyuki / Reeve, John

    Microbiology (Reading, England)

    2019  Volume 165, Issue 11, Page(s) 1166–1168

    Abstract: Thermococcus ... ...

    Abstract Thermococcus kodakarensis
    MeSH term(s) Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Genome, Bacterial ; Hydrogen/metabolism ; Phylogeny ; Thermococcus/classification ; Thermococcus/physiology ; Thermotolerance
    Chemical Substances Archaeal Proteins ; Hydrogen (7YNJ3PO35Z)
    Language English
    Publishing date 2019-10-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180712-x
    ISSN 1465-2080 ; 1350-0872
    ISSN (online) 1465-2080
    ISSN 1350-0872
    DOI 10.1099/mic.0.000839
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  5. Article ; Online: Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis.

    Kita, Akiko / Ishida, Yuna / Shimosaka, Takahiro / Michimori, Yuta / Makarova, Kira / Koonin, Eugene / Atomi, Haruyuki / Miki, Kunio

    Proteins

    2024  Volume 92, Issue 6, Page(s) 768–775

    Abstract: The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is ... ...

    Abstract The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures. Unusually, the archaeal DPCK utilizes GTP as the phosphate donor although the analogous bacterial and eukaryotic enzymes are ATP-dependent kinases. Here, we report the crystal structure of DPCK and its complex with GTP and a magnesium ion from the archaeal hyperthermophile Thermococcus kodakarensis. The crystal structure demonstrates why GTP is the preferred substrate of this kinase. We also report the activity analyses of site-directed mutants of crucial residues determined based on sequence conservation and the crystal structure. From these results, the key residues involved in the reaction of phosphoryl transfer and the possible dephospho-CoA binding site are inferred.
    MeSH term(s) Thermococcus/enzymology ; Thermococcus/genetics ; Thermococcus/chemistry ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Guanosine Triphosphate/chemistry ; Models, Molecular ; Phosphotransferases (Alcohol Group Acceptor)/chemistry ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Magnesium/metabolism ; Magnesium/chemistry ; Amino Acid Sequence ; Mutagenesis, Site-Directed ; Catalytic Domain ; Binding Sites ; Substrate Specificity ; Coenzyme A/metabolism ; Coenzyme A/chemistry ; Protein Binding
    Chemical Substances Guanosine Triphosphate (86-01-1) ; Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; Archaeal Proteins ; dephospho-CoA kinase (EC 2.7.1.24) ; Magnesium (I38ZP9992A) ; Coenzyme A (SAA04E81UX)
    Language English
    Publishing date 2024-01-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.26666
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    Zs.A 2291: Show issues Location:
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  6. Article ; Online: A Lipoate-Protein Ligase Is Required for

    Jin, Jian-Qiang / Sato, Takaaki / Hachisuka, Shin-Ichi / Atomi, Haruyuki

    Applied and environmental microbiology

    2022  Volume 88, Issue 13, Page(s) e0064422

    Abstract: Lipoic acid is an organosulfur cofactor essential for several key enzyme complexes in oxidative and one-carbon metabolism. It is covalently bound to the lipoyl domain of the E2 subunit in some 2-oxoacid dehydrogenase complexes and the H-protein in the ... ...

    Abstract Lipoic acid is an organosulfur cofactor essential for several key enzyme complexes in oxidative and one-carbon metabolism. It is covalently bound to the lipoyl domain of the E2 subunit in some 2-oxoacid dehydrogenase complexes and the H-protein in the glycine cleavage system. Lipoate-protein ligase (Lpl) is involved in the salvage of exogenous lipoate and attaches free lipoate to the E2 subunit or the H-protein in an ATP-dependent manner. In the hyperthermophilic archaeon Thermococcus kodakarensis, TK1234 and TK1908 are predicted to encode the N- and C-terminal regions of Lpl, respectively. TK1908 and TK1234 recombinant proteins form a heterodimer and together displayed significant ligase activity toward octanoate in addition to lipoate when a chemically synthesized octapeptide was used as the acceptor. The proteins also displayed activity toward other fatty acids, indicating broad fatty acid specificity. On the other hand, lipoyl synthase from T. kodakarensis only recognized octanoyl-peptide as a substrate. Examination of individual proteins indicated that the TK1908 protein alone was able to catalyze the ligase reaction although with a much lower activity. Gene disruption of TK1908 led to lipoate/serine auxotrophy, whereas TK1234 gene deletion did not. Acyl carrier protein homologs are not found on the archaeal genomes, and the TK1908/TK1234 protein complex did not utilize octanoyl-CoA, raising the possibility that the substrate of the ligase reaction is octanoic acid itself. Although Lpl has been considered as an enzyme involved in lipoate salvage, the results imply that in T. kodakarensis, the TK1908 and TK1234 proteins function in
    MeSH term(s) Peptide Synthases/genetics ; Protein Biosynthesis ; Substrate Specificity ; Thermococcus
    Chemical Substances Peptide Synthases (EC 6.3.2.-) ; lipoate-protein ligase (EC 6.3.2.-)
    Language English
    Publishing date 2022-06-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/aem.00644-22
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    Zs.B 201: Show issues Location:
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  7. Article ; Online: Structural Insight into [NiFe] Hydrogenase Maturation by Transient Complexes between Hyp Proteins.

    Miki, Kunio / Atomi, Haruyuki / Watanabe, Satoshi

    Accounts of chemical research

    2020  Volume 53, Issue 4, Page(s) 875–886

    Abstract: NiFe] hydrogenases catalyze reversible hydrogen production/consumption. The core unit of [NiFe] hydrogenase consists of a large and a small subunit. The active site of the large subunit of [NiFe] hydrogenases contains a NiFe(CN) ...

    Abstract [NiFe] hydrogenases catalyze reversible hydrogen production/consumption. The core unit of [NiFe] hydrogenase consists of a large and a small subunit. The active site of the large subunit of [NiFe] hydrogenases contains a NiFe(CN)
    MeSH term(s) Biocatalysis ; Hydrogenase/chemistry ; Hydrogenase/metabolism ; Protein Binding
    Chemical Substances nickel-iron hydrogenase (EC 1.12.-) ; Hydrogenase (EC 1.12.7.2)
    Language English
    Publishing date 2020-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1483291-4
    ISSN 1520-4898 ; 0001-4842
    ISSN (online) 1520-4898
    ISSN 0001-4842
    DOI 10.1021/acs.accounts.0c00022
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  8. Article ; Online: Metabolism: Nothing to waste.

    Atomi, Haruyuki

    Nature chemical biology

    2012  Volume 8, Issue 11, Page(s) 877–878

    MeSH term(s) Adenosine/analogs & derivatives ; Adenosine/metabolism ; Methionine/metabolism ; Molecular Structure ; Polyamines/metabolism ; Rhodospirillum rubrum/enzymology ; Rhodospirillum rubrum/metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; Sulfhydryl Compounds/metabolism ; Terpenes/metabolism ; Thionucleosides/metabolism
    Chemical Substances Polyamines ; Sulfhydryl Compounds ; Terpenes ; Thionucleosides ; methylmercaptan (2X8406WW9I) ; 2-methylthioadenosine (4105-39-9) ; Methionine (AE28F7PNPL) ; Ribulose-Bisphosphate Carboxylase (EC 4.1.1.39) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2012-09-01
    Publishing country United States
    Document type News
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/nchembio.1089
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  9. Article ; Online: Regulation of thermoregulatory behavior by commensal bacteria in Drosophila.

    Suito, Takuto / Nagao, Kohjiro / Juni, Naoto / Hara, Yuji / Sokabe, Takaaki / Atomi, Haruyuki / Umeda, Masato

    Bioscience, biotechnology, and biochemistry

    2022  Volume 86, Issue 8, Page(s) 1060–1070

    Abstract: Commensal bacteria affect many aspects of host physiology. In this study, we focused on the role of commensal bacteria in the thermoregulatory behavior of Drosophila melanogaster. We demonstrated that the elimination of commensal bacteria caused an ... ...

    Abstract Commensal bacteria affect many aspects of host physiology. In this study, we focused on the role of commensal bacteria in the thermoregulatory behavior of Drosophila melanogaster. We demonstrated that the elimination of commensal bacteria caused an increase in the preferred temperature of Drosophila third-instar larvae without affecting the activity of transient receptor potential ankyrin 1 (TRPA1)-expressing thermosensitive neurons. We isolated eight bacterial strains from the gut and culture medium of conventionally reared larvae and found that the preferred temperature of the larvae was decreased by mono-association with Lactobacillus plantarum or Corynebacterium nuruki. Mono-association with these bacteria did not affect the indices of energy metabolism such as ATP and glucose levels of larvae, which are closely linked to thermoregulation in animals. Thus, we show a novel role for commensal bacteria in host thermoregulation and identify two bacterial species that affect thermoregulatory behavior in Drosophila.
    MeSH term(s) Animals ; Bacteria ; Body Temperature Regulation ; Drosophila ; Drosophila melanogaster/microbiology ; Drosophila melanogaster/physiology ; Larva/physiology ; Symbiosis
    Language English
    Publishing date 2022-06-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1106450-x
    ISSN 1347-6947 ; 0916-8451
    ISSN (online) 1347-6947
    ISSN 0916-8451
    DOI 10.1093/bbb/zbac087
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    Zs.A 4647: Show issues Location:
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  10. Article ; Online: Altering the Phosphorylation Position of Pyrophosphate-Dependent

    Tashiro, Ryo / Sato, Takaaki / Atomi, Haruyuki / Miki, Kunio / Fujihashi, Masahiro

    ACS chemical biology

    2021  Volume 16, Issue 5, Page(s) 794–799

    Abstract: Most kinases utilize ATP as a phosphate donor and phosphorylate a wide range of phosphate acceptors. An alternative phosphate donor is inorganic pyrophosphate (PPi), which costs only 1/1000 of ATP. To develop a method to engineer PPi-dependent kinases, ... ...

    Abstract Most kinases utilize ATP as a phosphate donor and phosphorylate a wide range of phosphate acceptors. An alternative phosphate donor is inorganic pyrophosphate (PPi), which costs only 1/1000 of ATP. To develop a method to engineer PPi-dependent kinases, we herein aimed to alter the product of PPi-dependent
    MeSH term(s) Catalytic Domain ; Crystallization ; Diphosphates/chemistry ; Inositol Phosphates/chemistry ; Kinetics ; Magnetic Resonance Spectroscopy ; Mutant Proteins/chemistry ; Mutation ; Phosphoric Monoester Hydrolases/chemistry ; Phosphorylation ; Protein Conformation ; Tandem Mass Spectrometry ; Thermotoga maritima/enzymology
    Chemical Substances Diphosphates ; Inositol Phosphates ; Mutant Proteins ; inositol 1-phosphate (15421-51-9) ; inositol 3-phosphate (2831-74-5) ; diphosphoric acid (4E862E7GRQ) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2) ; myo-inositol-1 (or 4)-monophosphatase (EC 3.1.3.25)
    Language English
    Publishing date 2021-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.0c00733
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