{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:59:17Z","timestamp":1774317557609,"version":"3.50.1"},"reference-count":68,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T00:00:00Z","timestamp":1738886400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR51982\/NER\/95\/2011\/2023"],"award-info":[{"award-number":["BT\/PR51982\/NER\/95\/2011\/2023"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["febs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The FEBS Journal"],"published-print":{"date-parts":[[2025,5]]},"abstract":"<jats:p>\n                    Nucleolar essential protein 1 (Nep1; also known as ribosomal RNA small subunit methyltransferase Nep1) is a crucial factor in forming small ribosomal subunits in eukaryotes and archaea. Nep1 possesses an S\u2010adenosyl\u2010L\u2010methionine (SAM)\u2010dependent SpoU\u2010TrmD (SPOUT) ribosomal RNA (rRNA) methyltransferase (MTase) fold and catalyzes pseudouridine (\u03a8) methylation at specific sites of the small subunit (SSU) rRNA. Mutations in Nep1 proteins result in a severe developmental disorder in humans and reduced growth in yeast, suggesting its role in ribosome biogenesis. In this study, the crystal structures of Nep1 from the archaebacterium\n                    <jats:italic>Pyrococcus horikoshii<\/jats:italic>\n                    (\n                    <jats:italic>Ph<\/jats:italic>\n                    Nep1), both in its apo and holo (adenosine or 5\u2010methylthioadenosine bound) forms have been reported. The structural analysis of\n                    <jats:italic>Ph<\/jats:italic>\n                    Nep1 revealed an \u03b1\/\u03b2 fold featuring a deep trefoil knot akin to the SPOUT domain, with two novel extensions\u2014a globular loop and a \u03b2\u2013\u03b1\u2013\u03b2 extension. Moreover, the cofactor\u2010binding site of\n                    <jats:italic>Ph<\/jats:italic>\n                    Nep1 exhibits a preformed pocket, topologically similar to that of other SPOUT\u2010class MTases. Further, structural analysis of\n                    <jats:italic>Ph<\/jats:italic>\n                    Nep1 revealed that it forms a homodimer coordinated by inter\u2010subunit hydrogen bonds and hydrophobic interactions. Moreover, the results of this study indicate that\n                    <jats:italic>Ph<\/jats:italic>\n                    Nep1 can specifically methylate consensus RNAs, having a pseudouridine (\u03c8) located at position 926 of helix 35 (h35) of 16S rRNA in\n                    <jats:italic>P. horikoshii<\/jats:italic>\n                    . The stability of the Nep1\u2013RNA complex seems to be primarily assisted by the conserved arginine residues located at the dimeric interface.\n                  <\/jats:p>","DOI":"10.1111\/febs.70005","type":"journal-article","created":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T08:10:36Z","timestamp":1738915836000},"page":"2338-2358","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Structural analysis of the ribosome assembly factor Nep1, an\n                    <scp>N1<\/scp>\n                    \u2010specific pseudouridine methyltransferase, reveals mechanistic insights"],"prefix":"10.1111","volume":"292","author":[{"given":"Sayan","family":"Saha","sequence":"first","affiliation":[{"name":"Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati  India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9179-5723","authenticated-orcid":false,"given":"Shankar Prasad","family":"Kanaujia","sequence":"additional","affiliation":[{"name":"Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati  India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,2,7]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2008.09.024"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(02)02109-6"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00013-07"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(93)90120-F"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81308-2"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80238-X"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2007.05.012"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/0014-5793(75)80341-3"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1261\/rna.1724409"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/23.13.2548"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.12.11.3644"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1042\/bj1690071"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.33.1.261"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00294-001-0269-4"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2009.04.017"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp1189"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq931"},{"key":"e_1_2_11_19_1","first-page":"71","article-title":"SPOUT: 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