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Three structural proteins form the stable core of the rixosome to which three enzymatic modules are flexibly tethered including an RNA processing module, AAA-ATPase, and SUMO protease. The RNA processing module is formed by RNase PNK, a tetrameric assembly comprising two copies each of the LAS1L endoribonuclease (RNase) and the NOL9 polynucleotide kinase (PNK). Using single particle cryo-EM, we determined ATP\u03b3S and AMP\u2013PNP\/RNA-bound structures of human RNase PNK. The structures revealed the overall butterfly-like architecture of the complex and provide new insights into the mechanism of RNA accommodation and 5\u2032 hydroxyl phosphorylation within the NOL9 active site. Through reconstitution studies and molecular modeling, we establish how RNase PNK is incorporated into the larger rixosome complex by a distinct domain of LAS1L. Finally, we show that the human 5\u2032\u20133\u2032 exoribonuclease XRN2 directly associates with RNase PNK and selectively degrades NOL9-phosphorylated RNA in vitro, thereby linking ITS2 processing by the rixosome to processive exonucleolytic decay. Collectively this work establishes an updated model for how the rixosome integrates its diverse enzymatic activities to regulate ITS2 processing.<\/jats:p>","DOI":"10.1093\/nar\/gkag826","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T11:12:32Z","timestamp":1786101152000},"source":"Crossref","is-referenced-by-count":0,"title":["Structural insights into RNA phosphorylation by the RNase PNK module of the human rixosome complex"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7199-7416","authenticated-orcid":false,"given":"Jacob","family":"Gordon","sequence":"first","affiliation":[{"name":"Molecular and Cellular Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , 111 T. W. Alexander Drive, Research Triangle Park, NC 27709 ,","place":["United States"]},{"name":"Cambridge Institute for Medical Research , Cambridge CB2 0XY ,","place":["United Kingdom"]},{"name":"Department of Haematology, University of Cambridge , Cambridge CB2 0AW ,","place":["United Kingdom"]},{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge CB2 0AW ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Savannah M","family":"Seely","sequence":"additional","affiliation":[{"name":"Molecular and Cellular Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , 111 T. W. 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Alexander Drive, Research Triangle Park, NC 27709 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wyatt A","family":"Peele","sequence":"additional","affiliation":[{"name":"Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , 111 T. W. Alexander Drive, Research Triangle Park, NC 27709 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario J","family":"Borgnia","sequence":"additional","affiliation":[{"name":"Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , 111 T. W. Alexander Drive, Research Triangle Park, NC 27709 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9277-4553","authenticated-orcid":false,"given":"Alan J","family":"Warren","sequence":"additional","affiliation":[{"name":"Cambridge Institute for Medical Research , Cambridge CB2 0XY ,","place":["United Kingdom"]},{"name":"Department of Haematology, University of Cambridge , Cambridge CB2 0AW ,","place":["United Kingdom"]},{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge CB2 0AW ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2106-3102","authenticated-orcid":false,"given":"Robin E","family":"Stanley","sequence":"additional","affiliation":[{"name":"Molecular and Cellular Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , 111 T. 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Alexander Drive, Research Triangle Park, NC 27709 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"2026090805165162600_B1","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/s41586-022-04598-0","article-title":"Rixosomal RNA degradation contributes to silencing of Polycomb target genes","volume":"604","author":"Zhou","year":"2022","journal-title":"Nature"},{"key":"2026090805165162600_B2","doi-asserted-by":"publisher","first-page":"eadh3892","DOI":"10.1126\/science.adh3892","article-title":"Principles of human pre-60S biogenesis","volume":"381","author":"Vanden\u00a0Broeck","year":"2023","journal-title":"Science"},{"key":"2026090805165162600_B3","doi-asserted-by":"publisher","first-page":"eadw4603","DOI":"10.1126\/sciadv.adw4603","article-title":"PELP1 coordinates the modular assembly and enzymatic activity of the rixosome 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