A monomer-dimer switch modulates the activity of plant adenosine kinase
Jazyk angličtina Země Velká Británie, Anglie Médium print
Typ dokumentu časopisecké články
Grantová podpora
IGA_PrF_2023_012
Czech Science Foundation
IGA_PrF_2025_011
Czech Science Foundation
PubMed
40063605
PubMed Central
PMC12369479
DOI
10.1093/jxb/eraf094
PII: 8068880
Knihovny.cz E-zdroje
- Klíčová slova
- Physcomitrella patens, Zea mays, Adenosine kinase, SnRK, crystal structure, cytokinin, overexpression, purine, riboside,
- MeSH
- adenosinkinasa * metabolismus genetika chemie MeSH
- Arabidopsis genetika enzymologie metabolismus MeSH
- kukuřice setá * enzymologie genetika metabolismus MeSH
- mechy * enzymologie genetika metabolismus MeSH
- multimerizace proteinu MeSH
- rostlinné proteiny * metabolismus genetika chemie MeSH
- substrátová specifita MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- adenosinkinasa * MeSH
- rostlinné proteiny * MeSH
Adenosine undergoes ATP-dependent phosphorylation catalyzed by adenosine kinase (ADK). In plants, ADK also phosphorylates cytokinin ribosides, transport forms of the hormone. Here, we investigated the substrate preferences, oligomeric states, and structures of ADKs from moss (Physcomitrella patens) and maize (Zea mays) alongside metabolomic and phenotypic analyses. We showed that dexamethasone-inducible ZmADK overexpressor lines in Arabidopsis can benefit from a higher number of lateral roots and larger root areas under nitrogen starvation. We discovered that maize and moss enzymes can form dimers upon increasing protein concentration, setting them apart from the monomeric human and protozoal ADKs. Structural and kinetic analyses revealed a catalytically inactive unique dimer. Within the dimer, both active sites are mutually blocked. The activity of moss ADKs, exhibiting a higher propensity to dimerize, was 10-fold lower compared with maize ADKs. Two monomeric structures in a ternary complex highlight the characteristic transition from an open to a closed state upon substrate binding. This suggests that the oligomeric state switch can modulate the activity of moss ADKs and probably other plant ADKs. Moreover, dimer association represents a novel negative feedback mechanism, helping to maintain steady levels of adenosine and AMP.
Department of Chemical Biology Faculty of Science Palacký University Olomouc CZ 77900 Czech Republic
Institute for Plant Science and Microbiology Universität Hamburg D 22609 Hamburg Germany
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Allen M, Qin W, Moreau F, Moffatt B.. 2002. Adenine phosphoribosyltransferase isoforms of Arabidopsis and their potential contributions to adenine and cytokinin metabolism. Physiologia Plantarum 115, 56–68. PubMed
Andres CM, Fox IH.. 1979. Purification and properties of human placental adenosine kinase. Journal of Biological Chemistry 254, 11388–11393. PubMed
Ashihara H, Stasolla C, Fujimura T, Crozier A.. 2018. Purine salvage in plants. Phytochemistry 147, 89–124. PubMed
Baccolini C, Witte CP.. 2019. AMP and GMP catabolism in Arabidopsis converge on xanthosine, which is degraded by a nucleoside hydrolase heterocomplex. The Plant Cell 31, 734–751. PubMed PMC
Bauer MR, Mackey MD.. 2019. Electrostatic complementarity as a fast and effective tool to optimize binding and selectivity of protein–ligand complexes. Journal of Medicinal Chemistry 62, 3036–3050. PubMed
Blondin C, Serina L, Wiesmüller L, Gilles AM, Bârzu O.. 1994. Improved spectrophotometric assay of nucleoside monophosphate kinase activity using the pyruvate kinase/lactate dehydrogenase coupling system. Analytical Biochemistry 220, 219–221. PubMed
Brautigam CA. 2015. Calculations and publication—quality illustrations for analytical ultracentrifugation data. Methods in Enzymology 562, 109–133. PubMed
Bricogne G, Blanc E, Brandl M, et al. 2011. BUSTER version 2.1.0. Cambridge: Global Phasing Ltd.
Bromley JR, Warnes BJ, Newell CA, Thomson JC, James CM, Turnbull CG, Hanke DE.. 2014. A purine nucleoside phosphorylase in PubMed
Burnstock G. 2007. Purine and pyrimidine receptors. Cellular and Molecular Life Sciences 64, 1471–1483. PubMed PMC
Cheeseright T, Mackey M, Rose S, Vinter A.. 2006. Molecular field extrema as descriptors of biological activity: definition and validation. Journal of Chemical Information and Modeling 46, 665–676. PubMed
Chen CM, Eckert RL.. 1977. Phosphorylation of cytokinin by adenosine kinase from wheat germ. Plant Physiology 59, 443–447. PubMed PMC
Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC.. 2010. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography 66, 12–21. PubMed PMC
Choi J, Tanaka K, Cao Y, Qi Y, Qiu J, Liang Y, Lee SY, Stacey G.. 2014. Identification of a plant receptor for extracellular ATP. Science 343, 290–294. PubMed
Cornelius S, Traub M, Bernard C, Salzig C, Lang P, Möhlmann T.. 2012. Nucleoside transport across the plasma membrane mediated by equilibrative nucleoside transporter 3 influences metabolism of Arabidopsis seedlings. Plant Biology 14, 696–705. PubMed
Darling JA, Sullivan WJ Jr, Carter D, Ullman B, Roos DS.. 1999. Recombinant expression, purification, and characterization of PubMed
Emsley P, Cowtan K.. 2004. Coot: model-building tools for molecular graphics. Acta Crystallographica. Section D, Biological Crystallography 60, 2126–2132. PubMed
Fisher MN, Newsholme EA.. 1984. Properties of rat heart adenosine kinase. The Biochemical Journal 221, 521–528. PubMed PMC
Girke C, Daumann M, Niopek-Witz S, Möhlmann T.. 2014. Nucleobase and nucleoside transport and integration into plant metabolism. Frontiers in Plant Science 5, 443. PubMed PMC
Guranowski A. 1979. Plant adenosine kinase: purification and some properties of the enzyme from PubMed
Halford NG, Hey SJ.. 2009. Snf1-related protein kinases (SnRKs) act within an intricate network that links metabolic and stress signalling in plants. The Biochemical Journal 419, 247–259. PubMed
Han BW, Bingman CA, Mahnke DK, Bannen RM, Bednarek SY, Sabina RL, Phillips GN Jr. 2006. Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1). Journal of Biological Chemistry 281, 14939–14947. PubMed
Hatch MD. 1966. Adenylosuccinate synthetase and adenylosuccinate lyase from plant tissues. The Biochemical Journal 98, 198–203. PubMed PMC
Hellsten Y, Maclean D, Rådegran G, Saltin B, Bangsbo J.. 1998. Adenosine concentrations in the interstitium of resting and contracting human skeletal muscle. Circulation 98, 6–8. PubMed
Hirose N, Takei K, Kuroha T, Kamada-Nobusada T, Hayashi H, Sakakibara H.. 2008. Regulation of cytokinin biosynthesis, compartmentalization and translocation. Journal of Experimental Botany 59, 75–83. PubMed
Iltzsch MH, Uber SS, Tankersley KO, el Kouni MH.. 1995. Structure–activity relationship for the binding of nucleoside ligands to adenosine kinase from PubMed
Janin J, Rodier F, Chakrabarti P, Bahadur RP.. 2007. Macromolecular recognition in the Protein Data Bank. Acta Crystallographica. Section D, Biological Crystallography 63, 1–8. PubMed PMC
Jung B, Flörchinger M, Kunz HH, Traub M, Wartenberg R, Jeblick W, Neuhaus HE, Möhlmann T.. 2009. Uridine-ribohydrolase is a key regulator in the uridine degradation pathway of Arabidopsis. The Plant Cell 21, 876–891. PubMed PMC
Jung B, Hoffmann C, Möhlmann T.. 2011. Arabidopsis nucleoside hydrolases involved in intracellular and extracellular degradation of purines. The Plant Journal 65, 703–711. PubMed
Kabsch W. 2010. XDS. Acta Crystallographica. Section D, Biological Crystallography 66, 125–132. PubMed PMC
Karlíková R, Široká J, Friedecký D, et al. 2016. Metabolite profiling of the plasma and leukocytes of chronic myeloid leukemia patients. Journal of Proteome Research 15, 3158–3166. PubMed
Karplus PA, Diederichs K.. 2012. Linking crystallographic model and data quality. Science 336, 1030–1033. PubMed PMC
Khakh BS, Burnstock G.. 2009. The double life of ATP. Scientific American 301, 84–90, 92. PubMed PMC
Končitíková R, Vigouroux A, Kopečná M, Andree T, Bartoš J, Šebela M, Moréra S, Kopečný D.. 2015. Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7. The Biochemical Journal 468, 109–123. PubMed
Kopečná M, Blaschke H, Kopečný D, Vigouroux A, Končitíková R, Novák O, Kotland O, Strnad M, Moréra S, von Schwartzenberg K.. 2013. Structure and function of nucleoside hydrolases from PubMed PMC
Kopečný DJ, Vigouroux A, Bělíček A, et al. 2025. Data from: A monomer–dimer switch modulates the activity of plant adenosine kinase. Dryad Digital Repository 10.5061/dryad.qrfj6q5sj PubMed DOI PMC
Kraft C, Deplazes A, Sohrmann M, Peter M.. 2008. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nature Cell Biology 10, 602–610. PubMed
Kuettel S, Greenwald J, Kostrewa D, Ahmed S, Scapozza L, Perozzo R.. 2011. Crystal structures of PubMed PMC
Kuhn M, Firth-Clark S, Tosco P, Mey ASJS, Mackey M, Michel J.. 2020. Assessment of binding affinity via alchemical free-energy calculations. Journal of Chemical Information and Modeling 60, 3120–3130. PubMed
Kuroha T, Tokunaga H, Kojima M, Ueda N, Ishida T, Nagawa S, Fukuda H, Sugimoto K, Sakakibara H.. 2009. Functional analyses of PubMed PMC
Kwade Z, Swiatek A, Azmi A, Goossens A, Inzé D, Van Onckelen H, Roef L.. 2005. Identification of four adenosine kinase isoforms in tobacco By-2 cells and their putative role in the cell cycle-regulated cytokinin metabolism. Journal of Biological Chemistry 280, 17512–17519. PubMed
Long MC, Escuyer V, Parker WB.. 2003. Identification and characterization of a unique adenosine kinase from PubMed PMC
Long MC, Parker WB.. 2006. Structure–activity relationship for nucleoside analogs as inhibitors or substrates of adenosine kinase from PubMed
Ľuptáková E, Vigouroux A, Končitíková R, et al. 2024. Plant nucleoside N-ribohydrolases: riboside binding and role in nitrogen storage mobilization. The Plant Journal 117, 1432–1452. PubMed
Manalastas-Cantos K, Konarev PV, Hajizadeh NR, et al. 2021. PubMed PMC
Martínez-Chantar ML, Vázquez-Chantada M, Garnacho M, et al. 2006. S-Adenosylmethionine regulates cytoplasmic HuR via AMP-activated kinase. Gastroenterology 131, 223–232. PubMed
Mathews II, Erion MD, Ealick SE.. 1998. Structure of human adenosine kinase at 1.5 Å resolution. Biochemistry 37, 15607–15620. PubMed
Melino VJ, Casartelli A, George J, Rupasinghe T, Roessner U, Okamoto M, Heuer S.. 2018. RNA catabolites contribute to the nitrogen pool and support growth recovery of wheat. Frontiers in Plant Science 9, 1539. PubMed PMC
Miller RL, Adamczyk DL, Miller WH.. 1979b. Adenosine kinase from rabbit liver. I. Purification by affinity chromatography and properties. Journal of Biological Chemistry 254, 2339–2345. PubMed
Miller RL, Adamczyk DL, Miller WH, Koszalka GW, Rideout JL, Beacham LM 3rd, Chao EY, Haggerty JJ, Krenitsky TA, Elion GB.. 1979a. Adenosine kinase from rabbit liver. II. Substrate and inhibitor specificity. Journal of Biological Chemistry 254, 2346–2352. PubMed
Moffatt B, Pethe C, Laloue M.. 1991. Metabolism of benzyladenine is impaired in a mutant of PubMed PMC
Moffatt B, Somerville C.. 1988. Positive selection for male-sterile mutants of Arabidopsis lacking adenine phosphoribosyl transferase activity. Plant Physiology 86, 1150–1154. PubMed PMC
Moffatt BA, Stevens YY, Allen MS, Snider JD, Pereira LA, Todorova MI, Summers PS, Weretilnyk EA, Martin-McCaffrey L, Wagner C.. 2002. Adenosine kinase deficiency is associated with developmental abnormalities and reduced transmethylation. Plant Physiology 128, 812–821. PubMed PMC
Moffatt BA, Wang L, Allen MS, Stevens YY, Qin W, Snider J, von Schwartzenberg K.. 2000. Adenosine kinase of Arabidopsis. Kinetic properties and gene expression. Plant Physiology 124, 1775–1785. PubMed PMC
Mohannath G, Jackel JN, Lee YH, Buchmann RC, Wang H, Patil V, Adams AK, Bisaro DM.. 2014. A complex containing SNF1-related kinase (SnRK1) and adenosine kinase in Arabidopsis. PLoS One 9, e87592. PubMed PMC
Mok DWS, Mok MC.. 2001. Cytokinin metabolism and action. Annual Review of Plant Physiology and Plant Molecular Biology 52, 89–118. PubMed
Muchmore SW, Smith RA, Stewart AO, et al. 2006. Crystal structures of human adenosine kinase inhibitor complexes reveal two distinct binding modes. Journal of Medicinal Chemistry 49, 6726–6731. PubMed
Pfefferkorn ER, Pfefferkorn LC.. 1976. Arabinosyl nucleosides inhibit PubMed
Plačková L, Okleštková J, Pospíšková K, et al. 2017. Microscale magnetic microparticle-based immunopurification of cytokinins from Arabidopsis root apex. The Plant Journal 89, 1065–1075. PubMed
Reddy MCM, Palaninathan SK, Shetty ND, Owen JL, Watson MD, Sacchettini JC.. 2007. High resolution crystal structures of PubMed
Redillas MCFR, Bang SW, Lee DK, Kim YS, Jung H, Chung PJ, Suh JW, Kim JK.. 2019. Allantoin accumulation through overexpression of ureide permease1 improves rice growth under limited nitrogen conditions. Plant Biotechnology Journal 17, 1289–1301. PubMed PMC
Romanello L, Bachega JF, Cassago A, Brandão-Neto J, DeMarco R, Garratt RC, Pereira HD.. 2013. Adenosine kinase from PubMed
Sakakibara H. 2006. Cytokinins: activity, biosynthesis, and translocation. Annual Review of Plant Biology 57, 431–449. PubMed
Sauter M, Moffatt B, Saechao MC, Hell R, Wirtz M.. 2013. Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. The Biochemical Journal 451, 145–154. PubMed
Schindelin J, Arganda-Carreras I, Frise E, et al. 2012. Fiji: an open-source platform for biological-image analysis. Nature Methods 9, 676–682. PubMed PMC
Schmülling T, Werner T, Riefler M, Krupková E, Bartrina y Manns I.. 2003. Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. Journal of Plant Research 116, 241–252. PubMed
Schoor S, Farrow S, Blaschke H, Lee S, Perry G, von Schwartzenberg K, Emery N, Moffatt B.. 2011. Adenosine kinase contributes to cytokinin interconversion in Arabidopsis. Plant Physiology 157, 659–672. PubMed PMC
Schuck P. 2000. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophysical Journal 78, 1606–1619. PubMed PMC
Schumacher MA, Scott DM, Mathews II, Ealick SE, Roos DS, Ullman B, Brennan RG.. 2000. Crystal structures of PubMed
Schwartzman JD, Pfefferkorn ER.. 1982. PubMed
Storoni LC, McCoy AJ, Read RJ.. 2004. Likelihood-enhanced fast rotation functions. Acta Crystallographica. Section D, Biological Crystallography 60, 432–438. PubMed
Stroganov OV, Novikov FN, Stroylov VS, Kulkov V, Chilov GG.. 2008. Lead finder: an approach to improve accuracy of protein–ligand docking, binding energy estimation, and virtual screening. Journal of Chemical Information and Modeling 48, 2371–2385. PubMed
Supíková K, Kosinová A, Vavruša M, Kopliková L, François A, Pospíšil J, Zatloukal M, Wever R, Hartog A, Grúz J.. 2022. Sulfated phenolic acids in plants. Planta 255, 124. PubMed
Svačinová J, Novák O, Plačková L, Lenobel R, Holík J, Strnad M, Doležal K.. 2012. A new approach for cytokinin isolation from Arabidopsis tissues using miniaturized purification: pipette tip solid-phase extraction. Plant Methods 8, 17. PubMed PMC
Tickle IJ, Flensburg C, Keller P, Paciorek W, Sharff A, Vonrhein C, Bricogne G.. 2016. STARANISO. Cambridge: Global Phasing Ltd, http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi
Timm J, González-Pacanowska D, Wilson KS.. 2014. Structures of adenosine kinase from PubMed PMC
Tranová L, Buček J, Zatloukal M, Cankař P, Stýskala J.. 2019. Synthesis of [ PubMed
van Leene J, Eeckhout D, Gadeyne A, et al. 2022. Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins. Nature Plants 8, 1245–1261. PubMed
Vodnala M, Fijolek A, Rofougaran R, Mosimann M, Mäser P, Hofer A.. 2008. Adenosine kinase mediates high affinity adenosine salvage in PubMed
von Schwartzenberg K, Kruse S, Reski R, Moffatt B, Laloue M.. 1998. Cloning and characterization of an adenosine kinase from PubMed
Wang H, Hao L, Shung CY, Sunter G, Bisaro DM.. 2003. Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. The Plant Cell 15, 3020–3032. PubMed PMC
Weretilnyk EA, Alexander KJ, Drebenstedt M, Snider JD, Summers PS, Moffatt BA.. 2001. Maintaining methylation activities during salt stress. The involvement of adenosine kinase. Plant Physiology 125, 856–865. PubMed PMC
Wielopolska A, Townley H, Moore I, Waterhouse P, Helliwell C.. 2005. A high-throughput inducible RNAi vector for plants. Plant Biotechnology Journal 3, 583–590. PubMed
Wormit A, Traub M, Flörchinger M, Neuhaus HE, Möhlmann T.. 2004. Characterization of three novel members of the PubMed PMC
Xu J, Zhang HY, Xie CH, Xue HW, Dijkhuis P, Liu CM.. 2005. PubMed
Yamada Y, Goto H, Ogasawara N.. 1980. Purification and properties of adenosine kinase from rat brain. Biochimica et Biophysica Acta 616, 199–207. PubMed
Zhang Y, El Kouni MH, Ealick SE.. 2007. Substrate analogs induce an intermediate conformational change in PubMed
Zrenner R, Stitt M, Sonnewald U, Boldt R.. 2006. Pyrimidine and purine biosynthesis and degradation in plants. Annual Review of Plant Biology 57, 805–836. PubMed
A monomer-dimer switch modulates the activity of plant adenosine kinase