ArticleNucleic acids research2005
Structure-function analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 61 citations in OpenAlex.
- DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function.Nucleic acids research · 2025Review
- Human DBR1 deficiency impairs stress granule-dependent PKR antiviral immunity.The Journal of experimental medicine · 2025Article
- Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition.Genes & development · 2024Article
- Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition.bioRxiv : the preprint server for biology · 2024Article
- An unknown essential function of tRNA splicing endonuclease is linked to the integrated stress response and intron debranching.Genetics · 2023Article
- Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.Biochemistry · 2022Article
- Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1.RNA (New York, N.Y.) · 2022Article
- Protein Aggregation in the Pathogenesis of Ischemic Stroke.Cellular and molecular neurobiology · 2021Review
- Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs.Molecular genetics and genomics : MGG · 2021Article
- Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3'-PO4 and 3'-OH termini.Nucleic acids research · 2021Article
- Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6.Genes & development · 2019Article
- Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.Journal of structural biology · 2019Review
- Manganese Is Essential for PlcP Metallophosphoesterase Activity Involved in Lipid Remodeling in Abundant Marine Heterotrophic Bacteria.Applied and environmental microbiology · 2018Article
- All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Unexplored Molecular Features of theFrontiers in cellular and infection microbiology · 2018Article
- Conformational Changes in the 5' End of the HIV-1 Genome Dependent on the Debranching Enzyme DBR1 during Early Stages of Infection.Journal of virology · 2017Article
- Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic ZnFEBS letters · 2017Article
- Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Mechanistic insights into the manganese-dependent phosphodiesterase activity of yeast Dbr1 with bis-p-nitrophenylphosphate and branched RNA substrates.RNA (New York, N.Y.) · 2016Article
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4 authors at 1 institution in 1 country.
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Abstract
Saccharomyces cerevisiae Dbr1 is a 405-amino acid RNA debranching enzyme that cleaves the 2'-5' phosphodiester bonds of the lariat introns formed during pre-mRNA splicing. Debranching appears to be a rate-limiting step for the turnover of intronic RNA, insofar as the steady-state levels of lariat introns are greatly increased in a Deltadbr1 strain. To gain insight to the requirements for yeast Dbr1 function, we performed a mutational analysis of 28 amino acids that are conserved in Dbr1 homologs from other organisms. We identified 13 residues (His13, Asp40, Arg45, Asp49, Tyr68, Tyr69, Asn85, His86, Glu87, His179, Asp180, His231 and His233) at which alanine substitutions resulted in lariat intron accumulation in vivo. Conservative replacements at these positions were introduced to illuminate structure-activity relationships. Residues important for Dbr1 function include putative counterparts of the amino acids that comprise the active site of the metallophosphoesterase superfamily, exemplified by the DNA phosphodiesterase Mre11. Using natural lariat RNAs and synthetic branched RNAs as substrates, we found that mutation of Asp40, Asn85, His86, His179, His231 or His233 to alanine abolishes or greatly diminishes debranching activity in vitro. Dbr1 sediments as a monomer and requires manganese as the metal cofactor for debranching.
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