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Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site
Recognition of the 5′ splice site by group II introns involves pairing between an exon binding sequence (EBS) 1 within the ID3 stem–loop of domain 1 and a complementary sequence at the 3′ end of exon 1 (IBS1). To identify the molecular basis for splice site definition of a group IIB ai5γ intron, we...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866642/ https://www.ncbi.nlm.nih.gov/pubmed/24243113 http://dx.doi.org/10.1261/rna.039701.113 |
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author | Popović, Milena Greenbaum, Nancy L. |
author_facet | Popović, Milena Greenbaum, Nancy L. |
author_sort | Popović, Milena |
collection | PubMed |
description | Recognition of the 5′ splice site by group II introns involves pairing between an exon binding sequence (EBS) 1 within the ID3 stem–loop of domain 1 and a complementary sequence at the 3′ end of exon 1 (IBS1). To identify the molecular basis for splice site definition of a group IIB ai5γ intron, we probed the solution structure of the ID3 stem–loop alone and upon binding of its IBS1 target by solution NMR. The ID3 stem was structured. The base of the ID3 loop was stacked but displayed a highly flexible EBS1 region. The flexibility of EBS1 appears to be a general feature of the ai5γ and the smaller Oceanobacillus iheyensis (O.i.) intron and may help in effective search of conformational space and prevent errors in splicing as a result of fortuitous base-pairing. Binding of IBS1 results in formation of a structured seven base pair duplex that terminates at the 5′ splice site in spite of the potential for additional A-U and G•U pairs. Comparison of these data with conformational features of EBS1–IBS1 duplexes extracted from published structures suggests that termination of the duplex and definition of the splice site are governed by constraints of the helical geometry within the ID3 loop. This feature and flexibility of the uncomplexed ID3 loop appear to be common for both the ai5γ and O.i. introns and may help to fine-tune elements of recognition in group II introns. |
format | Online Article Text |
id | pubmed-3866642 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-38666422015-01-01 Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site Popović, Milena Greenbaum, Nancy L. RNA Articles Recognition of the 5′ splice site by group II introns involves pairing between an exon binding sequence (EBS) 1 within the ID3 stem–loop of domain 1 and a complementary sequence at the 3′ end of exon 1 (IBS1). To identify the molecular basis for splice site definition of a group IIB ai5γ intron, we probed the solution structure of the ID3 stem–loop alone and upon binding of its IBS1 target by solution NMR. The ID3 stem was structured. The base of the ID3 loop was stacked but displayed a highly flexible EBS1 region. The flexibility of EBS1 appears to be a general feature of the ai5γ and the smaller Oceanobacillus iheyensis (O.i.) intron and may help in effective search of conformational space and prevent errors in splicing as a result of fortuitous base-pairing. Binding of IBS1 results in formation of a structured seven base pair duplex that terminates at the 5′ splice site in spite of the potential for additional A-U and G•U pairs. Comparison of these data with conformational features of EBS1–IBS1 duplexes extracted from published structures suggests that termination of the duplex and definition of the splice site are governed by constraints of the helical geometry within the ID3 loop. This feature and flexibility of the uncomplexed ID3 loop appear to be common for both the ai5γ and O.i. introns and may help to fine-tune elements of recognition in group II introns. Cold Spring Harbor Laboratory Press 2014-01 /pmc/articles/PMC3866642/ /pubmed/24243113 http://dx.doi.org/10.1261/rna.039701.113 Text en © 2013 Popović and Greenbaum; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/. |
spellingShingle | Articles Popović, Milena Greenbaum, Nancy L. Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title | Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title_full | Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title_fullStr | Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title_full_unstemmed | Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title_short | Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site |
title_sort | role of helical constraints of the ebs1–ibs1 duplex of a group ii intron on demarcation of the 5′ splice site |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866642/ https://www.ncbi.nlm.nih.gov/pubmed/24243113 http://dx.doi.org/10.1261/rna.039701.113 |
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