{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Denson JM"],"funding":["HHS | NIH | National Institute of General Medical Sciences","NIGMS NIH HHS","HHS | NIH | National Institute of General Medical Sciences (NIGMS)"],"pagination":["e2414980121"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11725892"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["122(1)"],"pubmed_abstract":["The TRAMP complex contains two enzymatic activities essential for RNA processing upstream of the nuclear exosome. Within TRAMP, RNA is 3' polyadenylated by a subcomplex of Trf4/5 and Air1/2 and unwound 3' to 5' by Mtr4, a DExH helicase. The molecular mechanisms of TRAMP assembly and RNA shuffling between the two TRAMP catalytic sites are poorly understood. Here, we report solution hydrogen-deuterium exchange data with thermodynamic and functional assays to uncover these mechanisms for yeast TRAMP with Trf4 and Air2 homologs. We show that TRAMP assembly constrains RNA-recognition motifs that are peripheral to catalytic sites. These include the Mtr4 Arch and Air2 zinc knuckles 1, 2, and 3. While the Air2 Arch-interacting motif likely constrains the Mtr4 Arch via transient interactions, these"],"journal":["Proceedings of the National Academy of Sciences of the United States of America"],"pubmed_title":["TRAMP assembly alters the conformation and RNA binding of Mtr4 and Trf4-Air2."],"pmcid":["PMC11725892"],"funding_grant_id":["R35 GM133751","R15GM148949","R01GM117311","R35GM133751","R01 GM117311","R15 GM148949"],"pubmed_authors":["Denson JM","Thompson K","Zhang N","Ball D","Johnson SJ","D'Arcy S"],"additional_accession":[]},"is_claimable":false,"name":"TRAMP assembly alters the conformation and RNA binding of Mtr4 and Trf4-Air2.","description":"The TRAMP complex contains two enzymatic activities essential for RNA processing upstream of the nuclear exosome. Within TRAMP, RNA is 3' polyadenylated by a subcomplex of Trf4/5 and Air1/2 and unwound 3' to 5' by Mtr4, a DExH helicase. The molecular mechanisms of TRAMP assembly and RNA shuffling between the two TRAMP catalytic sites are poorly understood. Here, we report solution hydrogen-deuterium exchange data with thermodynamic and functional assays to uncover these mechanisms for yeast TRAMP with Trf4 and Air2 homologs. We show that TRAMP assembly constrains RNA-recognition motifs that are peripheral to catalytic sites. These include the Mtr4 Arch and Air2 zinc knuckles 1, 2, and 3. While the Air2 Arch-interacting motif likely constrains the Mtr4 Arch via transient interactions, these","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jan","modification":"2026-06-01T16:01:34.305Z","creation":"2026-04-08T14:03:49.83Z"},"accession":"S-EPMC11725892","cross_references":{"pubmed":["39752526"],"doi":["10.1073/pnas.2414980121"]}}