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Kita A, Ishida Y, Shimosaka T, Michimori Y, Makarova K, Koonin E, Atomi H, Miki K. Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins 2024; 92:768-775. [PMID: 38235908 DOI: 10.1002/prot.26666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/19/2024]
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.
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Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Yuna Ishida
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kira Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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Kita A, Kishimoto A, Shimosaka T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K. Crystal structure of pantoate kinase from Thermococcus kodakarensis. Proteins 2019; 88:718-724. [PMID: 31697438 DOI: 10.1002/prot.25852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/29/2019] [Accepted: 11/03/2019] [Indexed: 11/09/2022]
Abstract
The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4'-phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.
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Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Asako Kishimoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hiroya Tomita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuusuke Yokooji
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,JST, CREST, Tokyo, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,JST, CREST, Tokyo, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.,JST, CREST, Tokyo, Japan
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An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research. Folia Microbiol (Praha) 2019; 65:67-78. [PMID: 31286382 DOI: 10.1007/s12223-019-00730-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
Abstract
Almost 25 years have passed since the discovery of a planktonic, heterotrophic, hyperthermophilic archaeon named Thermococcus kodakarensis KOD1, previously known as Pyrococcus sp. KOD1, by Imanaka and coworkers. T. kodakarensis is one of the most studied archaeon in terms of metabolic pathways, available genomic resources, established genetic engineering techniques, reporter constructs, in vitro transcription/translation machinery, and gene expression/gene knockout systems. In addition to all these, ease of growth using various carbon sources makes it a facile archaeal model organism. Here, in this review, an attempt is made to reflect what we have learnt from this hyperthermophilic archaeon.
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