{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T22:50:39Z","timestamp":1789685439682,"version":"4.0.1"},"reference-count":112,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T00:00:00Z","timestamp":1660694400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1937971"],"award-info":[{"award-number":["1937971"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM130135"],"award-info":[{"award-number":["R01 GM130135"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["jbc.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biological Chemistry"],"published-print":{"date-parts":[[2022,10]]},"DOI":"10.1016\/j.jbc.2022.102393","type":"journal-article","created":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T02:10:04Z","timestamp":1660788604000},"page":"102393","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":36,"title":["Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases"],"prefix":"10.1016","volume":"298","author":[{"given":"Sarah E.","family":"Strassler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isobel E.","family":"Bowles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debayan","family":"Dey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane E.","family":"Jackman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graeme L.","family":"Conn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jbc.2022.102393_bib1","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/S0968-0004(03)00090-2","article-title":"Many paths to methyltransfer: a chronicle of convergence","volume":"28","author":"Schubert","year":"2003","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jbc.2022.102393_bib2","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.1691","article-title":"RNA nucleotide methylation: 2021 update","volume":"13","author":"Motorin","year":"2022","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib3","doi-asserted-by":"crossref","first-page":"657","DOI":"10.2217\/epi.10.44","article-title":"Molecular coupling of DNA methylation and histone methylation","volume":"2","author":"Hashimoto","year":"2010","journal-title":"Epigenomics"},{"key":"10.1016\/j.jbc.2022.102393_bib4","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1261\/rna.049932.115","article-title":"tRNA processing, modification, and subcellular dynamics: past, present, and future","volume":"21","author":"Phizicky","year":"2015","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib5","doi-asserted-by":"crossref","first-page":"3473","DOI":"10.1021\/ct500107y","article-title":"Influence of sequence and covalent modifications on yeast tRNA dynamics","volume":"10","author":"Zhang","year":"2014","journal-title":"J.\u00a0Chem. Theor. Comput."},{"key":"10.1016\/j.jbc.2022.102393_bib6","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1016\/j.apsb.2020.08.011","article-title":"Diversity of the reaction mechanisms of SAM-dependent enzymes","volume":"11","author":"Sun","year":"2021","journal-title":"Acta Pharm. Sin B"},{"key":"10.1016\/j.jbc.2022.102393_bib7","series-title":"Comprehensive Toxicology","article-title":"4.21 - methyltransferases","author":"Lennard","year":"2010"},{"key":"10.1016\/j.jbc.2022.102393_bib8","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1016\/S0969-2126(96)00135-9","article-title":"The structure of the C-terminal domain of methionine synthase: Presenting S-adenosylmethionine for reductive methylation of B12","volume":"4","author":"Dixon","year":"1996","journal-title":"Structure"},{"key":"10.1016\/j.jbc.2022.102393_bib9","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/846","article-title":"The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase","volume":"5","author":"Schubert","year":"1998","journal-title":"Nat. Struct. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib10","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1107\/S0907444902006601","article-title":"An enzyme with a deep trefoil knot for the active-site architecture","volume":"58","author":"Nureki","year":"2002","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"10.1016\/j.jbc.2022.102393_bib11","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1016\/S0969-2126(02)00852-3","article-title":"The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot","volume":"10","author":"Michel","year":"2002","journal-title":"Structure"},{"key":"10.1016\/j.jbc.2022.102393_bib12","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/prot.10323","article-title":"Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot","volume":"51","author":"Lim","year":"2003","journal-title":"Proteins"},{"key":"10.1016\/j.jbc.2022.102393_bib13","doi-asserted-by":"crossref","first-page":"2593","DOI":"10.1093\/emboj\/cdg269","article-title":"Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition","volume":"22","author":"Ahn","year":"2003","journal-title":"EMBO J."},{"key":"10.1016\/j.jbc.2022.102393_bib14","first-page":"71","article-title":"Spout: A class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases","volume":"4","author":"Anantharaman","year":"2002","journal-title":"J.\u00a0Mol. Microbiol. Biotechnol."},{"key":"10.1016\/j.jbc.2022.102393_bib15","doi-asserted-by":"crossref","first-page":"E4197","DOI":"10.1073\/pnas.1422981112","article-title":"Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD","volume":"112","author":"Ito","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2022.102393_bib16","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/j.str.2004.03.003","article-title":"Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme","volume":"12","author":"Nureki","year":"2004","journal-title":"Structure"},{"key":"10.1016\/j.jbc.2022.102393_bib17","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/1471-2105-8-73","article-title":"Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases","volume":"8","author":"Tkaczuk","year":"2007","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.jbc.2022.102393_bib18","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1016\/j.jmb.2003.09.011","article-title":"Insights into catalysis by a knotted TrmD tRNA methyltransferase","volume":"333","author":"Elkins","year":"2003","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib19","doi-asserted-by":"crossref","first-page":"4093","DOI":"10.1093\/nar\/25.20.4093","article-title":"The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity","volume":"25","author":"Persson","year":"1997","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib20","doi-asserted-by":"crossref","DOI":"10.1038\/celldisc.2015.37","article-title":"Structural basis for Sfm1 functioning as a protein arginine methyltransferase","volume":"1","author":"Lv","year":"2015","journal-title":"Cell Discov."},{"key":"10.1016\/j.jbc.2022.102393_bib21","doi-asserted-by":"crossref","first-page":"23","DOI":"10.3390\/biom7010023","article-title":"Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA","volume":"7","author":"Hori","year":"2017","journal-title":"Biomolecules"},{"key":"10.1016\/j.jbc.2022.102393_bib22","doi-asserted-by":"crossref","first-page":"100","DOI":"10.3390\/genes10020100","article-title":"Insights into catalytic and tRNA recognition mechanism of the dual-specific tRNA methyltransferase from Thermococcus kodakarensis","volume":"10","author":"Krishnamohan","year":"2019","journal-title":"Genes (Basel)"},{"key":"10.1016\/j.jbc.2022.102393_bib23","doi-asserted-by":"crossref","first-page":"7828","DOI":"10.1093\/nar\/gkt568","article-title":"The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL","volume":"41","author":"Liu","year":"2013","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib24","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1261\/rna.044503.114","article-title":"Characterization of two homologous 2'-O-methyltransferases showing different specificities for their tRNA substrates","volume":"20","author":"Somme","year":"2014","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib25","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1261\/rna.5070303","article-title":"Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9","volume":"9","author":"Jackman","year":"2003","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib26","doi-asserted-by":"crossref","first-page":"6533","DOI":"10.1093\/nar\/gkq451","article-title":"New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA","volume":"38","author":"Kempenaers","year":"2010","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib27","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1471-2199-7-23","article-title":"The yfhQ gene of Escherichia coli encodes a tRNA:Cm32\/Um32 methyltransferase","volume":"7","author":"Purta","year":"2006","journal-title":"BMC Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib28","doi-asserted-by":"crossref","first-page":"25562","DOI":"10.1074\/jbc.M113.485128","article-title":"The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process","volume":"288","author":"Ochi","year":"2013","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib29","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1126\/science.2471265","article-title":"Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine","volume":"244","author":"Bjork","year":"1989","journal-title":"Science"},{"key":"10.1016\/j.jbc.2022.102393_bib30","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1038\/250546a0","article-title":"Structure of yeast phenylalanine tRNA at 3 A resolution","volume":"250","author":"Robertus","year":"1974","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2022.102393_bib31","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1101\/gad.1956510","article-title":"tRNA biology charges to the front","volume":"24","author":"Phizicky","year":"2010","journal-title":"Genes Dev."},{"key":"10.1016\/j.jbc.2022.102393_bib32","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.molcel.2005.10.036","article-title":"Rapid tRNA decay can result from lack of nonessential modifications","volume":"21","author":"Alexandrov","year":"2006","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2022.102393_bib33","doi-asserted-by":"crossref","first-page":"4287","DOI":"10.1016\/j.febslet.2014.09.038","article-title":"tRNA modifications regulate translation during cellular stress","volume":"588","author":"Gu","year":"2014","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jbc.2022.102393_bib34","doi-asserted-by":"crossref","first-page":"662620","DOI":"10.3389\/fmolb.2021.662620","article-title":"Toward an understanding of extracellular tRNA biology","volume":"8","author":"Torres","year":"2021","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.jbc.2022.102393_bib35","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/s41580-021-00342-0","article-title":"The expanding world of tRNA modifications and their disease relevance","volume":"22","author":"Suzuki","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib36","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1136\/jmedgenet-2014-102282","article-title":"TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly","volume":"51","author":"Gillis","year":"2014","journal-title":"J.\u00a0Med. Genet."},{"key":"10.1016\/j.jbc.2022.102393_bib37","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003888","article-title":"tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans","volume":"9","author":"Igoillo-Esteve","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jbc.2022.102393_bib38","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1084\/jem.20111075","article-title":"The 2'-O-methylation status of a single guanosine controls transfer RNA-mediated Toll-like receptor 7 activation or inhibition","volume":"209","author":"Jockel","year":"2012","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.jbc.2022.102393_bib39","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1080\/15476286.2016.1259781","article-title":"Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function","volume":"14","author":"Sloan","year":"2017","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib40","doi-asserted-by":"crossref","first-page":"7885","DOI":"10.1093\/nar\/gks508","article-title":"Impact of methylations of m2G966\/m5C967 in 16S rRNA on bacterial fitness and translation initiation","volume":"40","author":"Burakovsky","year":"2012","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib41","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1111\/j.1365-2958.2008.06485.x","article-title":"Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA","volume":"70","author":"Connolly","year":"2008","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jbc.2022.102393_bib42","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1093\/nar\/gkq931","article-title":"The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA","volume":"39","author":"Meyer","year":"2011","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib43","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1007\/s00294-001-0269-4","article-title":"Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis","volume":"40","author":"Eschrich","year":"2002","journal-title":"Curr. Genet."},{"key":"10.1016\/j.jbc.2022.102393_bib44","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1134\/S000629792011005X","article-title":"rRNA methylation and antibiotic resistance","volume":"85","author":"Osterman","year":"2020","journal-title":"Biochemistry (Mosc)"},{"key":"10.1016\/j.jbc.2022.102393_bib45","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.jmb.2004.10.051","article-title":"Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes","volume":"345","author":"Mosbacher","year":"2005","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib46","doi-asserted-by":"crossref","first-page":"26189","DOI":"10.1074\/jbc.M114.574780","article-title":"Binding induced RNA conformational changes control substrate recognition and catalysis by the thiostrepton resistance methyltransferase (Tsr)","volume":"289","author":"Kuiper","year":"2014","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib47","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1261\/rna.072090.119","article-title":"Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B","volume":"25","author":"Howell","year":"2019","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib48","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1093\/bioinformatics\/bti263","article-title":"ProtTest: selection of best-fit models of protein evolution","volume":"21","author":"Abascal","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jbc.2022.102393_bib49","doi-asserted-by":"crossref","first-page":"19714","DOI":"10.1073\/pnas.0805468105","article-title":"Stabilizing effect of knots on proteins","volume":"105","author":"Sulkowska","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2022.102393_bib50","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1038\/nsmb.3282","article-title":"Methyl transfer by substrate signaling from a knotted protein fold","volume":"23","author":"Christian","year":"2016","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib51","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/bs.enz.2017.03.003","article-title":"TrmD: a methyl transferase for tRNA methylation with m(1)G37","volume":"41","author":"Hou","year":"2017","journal-title":"Enzymes"},{"key":"10.1016\/j.jbc.2022.102393_bib52","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/nar\/gkt869","article-title":"Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate","volume":"42","author":"Shao","year":"2014","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib53","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1093\/nar\/gkv1369","article-title":"Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue","volume":"44","author":"Van Laer","year":"2016","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib54","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1261\/rna.2245910","article-title":"YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors","volume":"16","author":"Benitez-Paez","year":"2010","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib55","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1261\/rna.1198108","article-title":"YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA","volume":"14","author":"Purta","year":"2008","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib56","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/s41598-017-01186-5","article-title":"Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine","volume":"7","author":"Koh","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jbc.2022.102393_bib57","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.jmb.2012.08.016","article-title":"Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m(3)U1498) from crystal and solution structures","volume":"423","author":"Zhang","year":"2012","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib58","doi-asserted-by":"crossref","first-page":"7489","DOI":"10.1093\/nar\/gkv745","article-title":"tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily","volume":"43","author":"Liu","year":"2015","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib59","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1080\/15476286.2015.1050576","article-title":"Identification of determinants for tRNA substrate recognition by Escherichia coli C\/U34 2'-O-methyltransferase","volume":"12","author":"Zhou","year":"2015","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib60","doi-asserted-by":"crossref","first-page":"7388","DOI":"10.1016\/S0021-9258(18)34389-8","article-title":"A\u00a0thermostable tRNA (guanosine-2')-methyltransferase from Thermus thermophilus HB27 and the effect of ribose methylation on the conformational stability of tRNA","volume":"257","author":"Kumagai","year":"1982","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib61","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1046\/j.1365-2443.2002.00520.x","article-title":"Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs","volume":"7","author":"Hori","year":"2002","journal-title":"Genes Cells"},{"key":"10.1016\/j.jbc.2022.102393_bib62","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1017\/S1355838299981475","article-title":"The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs","volume":"5","author":"Cavaille","year":"1999","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib63","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1002\/prot.22065","article-title":"Crystal structure of the methyltransferase domain of human TARBP1","volume":"72","author":"Wu","year":"2008","journal-title":"Proteins"},{"key":"10.1016\/j.jbc.2022.102393_bib64","doi-asserted-by":"crossref","first-page":"34630","DOI":"10.1074\/jbc.M606141200","article-title":"Functional categorization of the conserved basic amino acid residues in TrmH (tRNA (Gm18) methyltransferase) enzymes","volume":"281","author":"Watanabe","year":"2006","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib65","doi-asserted-by":"crossref","first-page":"9018","DOI":"10.1074\/jbc.M109.065698","article-title":"Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes","volume":"285","author":"Ochi","year":"2010","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib66","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1107\/S1744309105022980","article-title":"Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus","volume":"61","author":"Pleshe","year":"2005","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun."},{"key":"10.1016\/j.jbc.2022.102393_bib67","doi-asserted-by":"crossref","first-page":"25721","DOI":"10.1074\/jbc.273.40.25721","article-title":"Substrate recognition of tRNA (Guanosine-2'-)-methyltransferase from Thermus thermophilus HB27","volume":"273","author":"Hori","year":"1998","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib68","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/oxfordjournals.jbchem.a123047","article-title":"Recognition sites of tRNA by a thermostable tRNA(guanosine-2'-)-methyltransferase from Thermus thermophilus HB27","volume":"107","author":"Matsumoto","year":"1990","journal-title":"J.\u00a0Biochem."},{"key":"10.1016\/j.jbc.2022.102393_bib69","doi-asserted-by":"crossref","first-page":"25081","DOI":"10.1074\/jbc.M212577200","article-title":"Aquifex aeolicus tRNA (Gm18) methyltransferase has unique substrate specificity. TRNA recognition mechanism of the enzyme","volume":"278","author":"Hori","year":"2003","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib70","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1261\/rna.2110805","article-title":"The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C\/D sRNP","volume":"11","author":"Renalier","year":"2005","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib71","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1016\/j.biochi.2005.02.004","article-title":"Two different mechanisms for tRNA ribose methylation in archaea: a short survey","volume":"87","author":"Clouet-d'Orval","year":"2005","journal-title":"Biochimie"},{"key":"10.1016\/j.jbc.2022.102393_bib72","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1093\/nar\/gkv1522","article-title":"Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon","volume":"44","author":"Kawamura","year":"2016","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib73","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1016\/j.jmb.2007.11.023","article-title":"Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA","volume":"375","author":"Kuratani","year":"2008","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib74","doi-asserted-by":"crossref","first-page":"7915","DOI":"10.1016\/S0021-9258(18)34268-6","article-title":"Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton","volume":"257","author":"Thompson","year":"1982","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib75","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1111\/j.1432-1033.1994.00431.x","article-title":"Overexpression of the thiostrepton-resistance gene from Streptomyces azureus in Escherichia coli and characterization of recognition sites of the 23S rRNA A1067 2'-methyltransferase in the guanosine triphosphatase center of 23S ribosomal RNA","volume":"224","author":"Bechthold","year":"1994","journal-title":"Eur. J. Biochem."},{"key":"10.1016\/j.jbc.2022.102393_bib76","doi-asserted-by":"crossref","first-page":"17013","DOI":"10.1074\/jbc.M901618200","article-title":"Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA","volume":"284","author":"Dunstan","year":"2009","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib77","article-title":"Substrate recognition and modification by the nosiheptide resistance methyltransferase","volume":"10","author":"Yin","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.jbc.2022.102393_bib78","doi-asserted-by":"crossref","first-page":"2346","DOI":"10.1128\/JB.186.8.2346-2354.2004","article-title":"Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth","volume":"186","author":"O'Dwyer","year":"2004","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.jbc.2022.102393_bib79","doi-asserted-by":"crossref","first-page":"8699","DOI":"10.1021\/bi9701538","article-title":"Interaction of tRNA with tRNA (guanosine-1)methyltransferase: binding specificity determinants involve the dinucleotide G36pG37 and tertiary structure","volume":"36","author":"Redlak","year":"1997","journal-title":"Biochemistry"},{"key":"10.1016\/j.jbc.2022.102393_bib80","doi-asserted-by":"crossref","first-page":"D159","DOI":"10.1093\/nar\/gkn772","article-title":"tRNAdb 2009: compilation of tRNA sequences and tRNA genes","volume":"37","author":"Juhling","year":"2009","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib81","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1111\/j.1365-2443.2006.01022.x","article-title":"The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus","volume":"11","author":"Takeda","year":"2006","journal-title":"Genes Cells"},{"key":"10.1016\/j.jbc.2022.102393_bib82","doi-asserted-by":"crossref","first-page":"9243","DOI":"10.1021\/bi049671q","article-title":"Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein","volume":"43","author":"Brule","year":"2004","journal-title":"Biochemistry"},{"key":"10.1016\/j.jbc.2022.102393_bib83","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.jmb.2007.08.010","article-title":"Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases","volume":"373","author":"Christian","year":"2007","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib84","doi-asserted-by":"crossref","first-page":"8058","DOI":"10.1021\/acscatal.0c00059","article-title":"Mg(2+)-Dependent methyl transfer by a knotted protein: a molecular dynamics simulation and quantum mechanics study","volume":"10","author":"Perlinska","year":"2020","journal-title":"ACS Catal."},{"key":"10.1016\/j.jbc.2022.102393_bib85","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1016\/j.chembiol.2014.07.023","article-title":"A\u00a0divalent metal ion-dependent N(1)-methyl transfer to G37-tRNA","volume":"21","author":"Sakaguchi","year":"2014","journal-title":"Chem. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib86","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1093\/nar\/gkp1189","article-title":"The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase","volume":"38","author":"Wurm","year":"2010","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib87","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1093\/jmcb\/mjq034","article-title":"Crystal structure of Mj1640\/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase","volume":"2","author":"Chen","year":"2010","journal-title":"J.\u00a0Mol. Cell Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib88","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1093\/nar\/gkq1131","article-title":"Structural insight into the functional mechanism of Nep1\/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis","volume":"39","author":"Thomas","year":"2011","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib89","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1261\/rna.2283106","article-title":"Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family","volume":"12","author":"Basturea","year":"2006","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib90","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1261\/rna.700507","article-title":"Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE","volume":"13","author":"Basturea","year":"2007","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib91","doi-asserted-by":"crossref","first-page":"6275","DOI":"10.1073\/pnas.1402789111","article-title":"Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA","volume":"111","author":"Dunkle","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2022.102393_bib92","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1261\/rna.030841.111","article-title":"The archaeal COG1901\/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA","volume":"18","author":"Chatterjee","year":"2012","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib93","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1080\/15476286.2015.1008358","article-title":"Diversity in mechanism and function of tRNA methyltransferases","volume":"12","author":"Swinehart","year":"2015","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib94","doi-asserted-by":"crossref","first-page":"6157","DOI":"10.1093\/nar\/gkaa353","article-title":"Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B","volume":"48","author":"Vilardo","year":"2020","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib95","doi-asserted-by":"crossref","first-page":"11583","DOI":"10.1093\/nar\/gks910","article-title":"A\u00a0subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis","volume":"40","author":"Vilardo","year":"2012","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib96","doi-asserted-by":"crossref","first-page":"9019","DOI":"10.1093\/nar\/gkx620","article-title":"Mechanistic features of the atypical tRNA m1G9 SPOUT methyltransferase, Trm10","volume":"45","author":"Krishnamohan","year":"2017","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib97","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1261\/rna.064345.117","article-title":"Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism","volume":"24","author":"Singh","year":"2018","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib98","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1038\/s41594-021-00637-y","article-title":"Structural basis of RNA processing by human mitochondrial RNase P","volume":"28","author":"Bhatta","year":"2021","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib99","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1261\/rna.1186608","article-title":"Identification of pseudouridine methyltransferase in Escherichia coli","volume":"14","author":"Ero","year":"2008","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib100","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1261\/rna.2234310","article-title":"Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD","volume":"16","author":"Ero","year":"2010","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2022.102393_bib101","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1021\/acschembio.5b00781","article-title":"Structural chemistry of human RNA methyltransferases","volume":"11","author":"Schapira","year":"2016","journal-title":"ACS Chem. Biol."},{"key":"10.1016\/j.jbc.2022.102393_bib102","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/1471-2105-4-9","article-title":"Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures","volume":"4","author":"Kurowski","year":"2003","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.jbc.2022.102393_bib103","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1093\/nar\/gkm1172","article-title":"The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site","volume":"36","author":"Taylor","year":"2008","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib104","doi-asserted-by":"crossref","first-page":"17642","DOI":"10.1074\/jbc.RA119.011181","article-title":"Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition","volume":"294","author":"Nosrati","year":"2019","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib105","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00077-17","article-title":"Substrate recognition and modification by a pathogen-associated aminoglycoside resistance 16S rRNA methyltransferase","volume":"61","author":"Vinal","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.jbc.2022.102393_bib106","doi-asserted-by":"crossref","first-page":"12862","DOI":"10.1074\/jbc.RA117.001286","article-title":"Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes","volume":"293","author":"Oerum","year":"2018","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib107","doi-asserted-by":"crossref","first-page":"3784","DOI":"10.1093\/nar\/29.18.3784","article-title":"AdoMet-dependent methylation, DNA methyltransferases and base flipping","volume":"29","author":"Cheng","year":"2001","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jbc.2022.102393_bib108","article-title":"50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA","author":"Laughlin","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.jbc.2022.102393_bib109","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1126\/science.284.5417.1171","article-title":"Crystal structure of a conserved ribosomal protein-RNA complex","volume":"284","author":"Conn","year":"1999","journal-title":"Science"},{"key":"10.1016\/j.jbc.2022.102393_bib110","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1093\/oxfordjournals.jbchem.a122933","article-title":"Effects of modification of 4-thiouridine in E. coli tRNA(fMet) on its methyl acceptor activity by thermostable Gm-methylases","volume":"106","author":"Hori","year":"1989","journal-title":"J.\u00a0Biochem."},{"key":"10.1016\/j.jbc.2022.102393_bib111","doi-asserted-by":"crossref","first-page":"28731","DOI":"10.1074\/jbc.M002174200","article-title":"Hypermodification of tRNA in thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii","volume":"275","author":"Bai","year":"2000","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jbc.2022.102393_bib112","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0088222","article-title":"Secondary structures of rRNAs from all three domains of life","volume":"9","author":"Petrov","year":"2014","journal-title":"PLoS One"}],"container-title":["Journal of Biological Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925822008365?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925822008365?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T16:37:33Z","timestamp":1762187853000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0021925822008365"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10]]},"references-count":112,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2022,10]]}},"alternative-id":["S0021925822008365"],"URL":"https:\/\/doi.org\/10.1016\/j.jbc.2022.102393","relation":{},"ISSN":["0021-9258"],"issn-type":[{"value":"0021-9258","type":"print"}],"subject":[],"published":{"date-parts":[[2022,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases","name":"articletitle","label":"Article Title"},{"value":"Journal of Biological Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jbc.2022.102393","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"102393"}}