The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase
The exosome is a conserved multi‐subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10‐subunit core complex of the exosome (Exo‐10) physically and functionally interacts with the Rrp6 exoribonuclease...
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| creator | Schuch, Benjamin Feigenbutz, Monika Makino, Debora L Falk, Sebastian Basquin, Claire Mitchell, Phil Conti, Elena |
| description | The exosome is a conserved multi‐subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10‐subunit core complex of the exosome (Exo‐10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo‐10
in vitro
is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N‐terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N‐terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C‐terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.
Synopsis
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.
The N‐terminal domains of
S. cerevisiae
Rrp6 and Rrp47 form a highly intertwined structural unit.
The Rrp6–Rrp47 complex creates a composite and conserved surface groove that binds the N‐terminus of Mtr4 and recruits Mtr4 to the nuclear exosome.
Structure‐based mutations of conserved residues within Rrp6 and Mtr4 disrupt their interaction, result in 5.8S RNA processing defects
in vivo
and inhibit growth of strains expressing a C‐terminal GFP fusion of Mtr4.
Graphical Abstract
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47. |
| doi_str_mv | 10.15252/embj.201488757 |
| format | Article |
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in vitro
is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N‐terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N‐terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C‐terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.
Synopsis
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.
The N‐terminal domains of
S. cerevisiae
Rrp6 and Rrp47 form a highly intertwined structural unit.
The Rrp6–Rrp47 complex creates a composite and conserved surface groove that binds the N‐terminus of Mtr4 and recruits Mtr4 to the nuclear exosome.
Structure‐based mutations of conserved residues within Rrp6 and Mtr4 disrupt their interaction, result in 5.8S RNA processing defects
in vivo
and inhibit growth of strains expressing a C‐terminal GFP fusion of Mtr4.
Graphical Abstract
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.</description><identifier>ISSN: 0261-4189</identifier><identifier>EISSN: 1460-2075</identifier><identifier>DOI: 10.15252/embj.201488757</identifier><identifier>PMID: 25319414</identifier><identifier>CODEN: EMJODG</identifier><language>eng</language><publisher>London: Blackwell Publishing Ltd</publisher><subject>Blotting, Western ; Calorimetry ; Chromatography, Gel ; Crystallization ; Crystallography ; DEAD-box RNA Helicases - chemistry ; DEAD-box RNA Helicases - metabolism ; DNA-Binding Proteins - chemistry ; DNA-Binding Proteins - metabolism ; Electrophoresis, Polyacrylamide Gel ; EMBO36 ; EMBO40 ; Enzymes ; Escherichia coli ; Exosome Multienzyme Ribonuclease Complex - chemistry ; Exosome Multienzyme Ribonuclease Complex - metabolism ; Fluorescence Polarization ; Models, Molecular ; Molecular biology ; Multiprotein Complexes - chemistry ; Multiprotein Complexes - metabolism ; Mutation ; nuclear exosome ; Nuclear Proteins - chemistry ; Nuclear Proteins - metabolism ; Oligonucleotide Probes ; Protein Conformation ; Ribonucleic acid ; RNA ; RNA degradation ; RNA-Binding Proteins - chemistry ; RNA-Binding Proteins - metabolism ; Rosaniline Dyes ; Saccharomyces cerevisiae - genetics ; Saccharomyces cerevisiae Proteins - chemistry ; Saccharomyces cerevisiae Proteins - metabolism ; X-ray crystallography ; yeast genetics ; Yeasts</subject><ispartof>The EMBO journal, 2014-12, Vol.33 (23), p.2829-2846</ispartof><rights>The Authors 2014</rights><rights>2014 The Authors</rights><rights>2014 The Authors.</rights><rights>2014 EMBO</rights><rights>2014 The Authors 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6177-d5d36b0fb213212bcf5cf3504294cd5308e35cc2210c63878c469e61bf32e71c3</citedby><cites>FETCH-LOGICAL-c6177-d5d36b0fb213212bcf5cf3504294cd5308e35cc2210c63878c469e61bf32e71c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282559/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282559/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1411,1427,27903,27904,41099,42168,45553,45554,46387,46811,51554,53769,53771</link.rule.ids><linktorsrc>$$Uhttps://doi.org/10.15252/embj.201488757$$EView_record_in_Springer_Nature$$FView_record_in_$$GSpringer_Nature</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25319414$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schuch, Benjamin</creatorcontrib><creatorcontrib>Feigenbutz, Monika</creatorcontrib><creatorcontrib>Makino, Debora L</creatorcontrib><creatorcontrib>Falk, Sebastian</creatorcontrib><creatorcontrib>Basquin, Claire</creatorcontrib><creatorcontrib>Mitchell, Phil</creatorcontrib><creatorcontrib>Conti, Elena</creatorcontrib><title>The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase</title><title>The EMBO journal</title><addtitle>EMBO J</addtitle><addtitle>EMBO J</addtitle><description>The exosome is a conserved multi‐subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10‐subunit core complex of the exosome (Exo‐10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo‐10
in vitro
is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N‐terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N‐terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C‐terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.
Synopsis
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.
The N‐terminal domains of
S. cerevisiae
Rrp6 and Rrp47 form a highly intertwined structural unit.
The Rrp6–Rrp47 complex creates a composite and conserved surface groove that binds the N‐terminus of Mtr4 and recruits Mtr4 to the nuclear exosome.
Structure‐based mutations of conserved residues within Rrp6 and Mtr4 disrupt their interaction, result in 5.8S RNA processing defects
in vivo
and inhibit growth of strains expressing a C‐terminal GFP fusion of Mtr4.
Graphical Abstract
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.</description><subject>Blotting, Western</subject><subject>Calorimetry</subject><subject>Chromatography, Gel</subject><subject>Crystallization</subject><subject>Crystallography</subject><subject>DEAD-box RNA Helicases - chemistry</subject><subject>DEAD-box RNA Helicases - metabolism</subject><subject>DNA-Binding Proteins - chemistry</subject><subject>DNA-Binding Proteins - metabolism</subject><subject>Electrophoresis, Polyacrylamide Gel</subject><subject>EMBO36</subject><subject>EMBO40</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Exosome Multienzyme Ribonuclease Complex - chemistry</subject><subject>Exosome Multienzyme Ribonuclease Complex - metabolism</subject><subject>Fluorescence Polarization</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>Multiprotein Complexes - chemistry</subject><subject>Multiprotein Complexes - metabolism</subject><subject>Mutation</subject><subject>nuclear exosome</subject><subject>Nuclear Proteins - chemistry</subject><subject>Nuclear Proteins - metabolism</subject><subject>Oligonucleotide Probes</subject><subject>Protein Conformation</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA degradation</subject><subject>RNA-Binding Proteins - chemistry</subject><subject>RNA-Binding Proteins - metabolism</subject><subject>Rosaniline Dyes</subject><subject>Saccharomyces cerevisiae - genetics</subject><subject>Saccharomyces cerevisiae Proteins - chemistry</subject><subject>Saccharomyces cerevisiae Proteins - metabolism</subject><subject>X-ray crystallography</subject><subject>yeast genetics</subject><subject>Yeasts</subject><issn>0261-4189</issn><issn>1460-2075</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtv1DAUhSMEokNhzQ5ZYsMmrd9OWCDRB4WqLQgVIbGxHOdmxkMSD3YC7b_HIWU0ICFWtnS_c-65Oln2lOADIqigh9BV6wOKCS8KJdS9bEG4xDnFStzPFphKknNSlHvZoxjXGGNRKPIw26OCkZITvsjq6xUguPHRd5BXrq9dv0SNsYMPEX0MG4lMX08frlDjQ4cMsr7b-OgGQHEMCYVpgALYMLphkg_J8nIIHK2gddZEeJw9aEwb4cndu599enN6ffw2v3h_9u749UVuJVEqr0XNZIWbihJGCa1sI2zDBOa05LYWDBfAhLWUEmwlK1RhuSxBkqphFBSxbD97NftuxqqD2kI_BNPqTXCdCbfaG6f_nPRupZf-u-a0oEKUyeDFnUHw30aIg-5ctNC2pgc_Rk0kLcu0mpGEPv8LXfsx9Om8iSoKzomQiTqcKRt8jAGabRiC9a8G9dSg3jaYFM92b9jyvytLwMsZ-OFauP2fnz69PDrfdcezOCZdv4Swk_qfgfJZ4uIAN9t9JnzVUjEl9OerM_3h6vzohLMv-oT9BLuVxv4</recordid><startdate>20141201</startdate><enddate>20141201</enddate><creator>Schuch, Benjamin</creator><creator>Feigenbutz, Monika</creator><creator>Makino, Debora L</creator><creator>Falk, Sebastian</creator><creator>Basquin, Claire</creator><creator>Mitchell, Phil</creator><creator>Conti, Elena</creator><general>Blackwell Publishing Ltd</general><general>Nature Publishing Group UK</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20141201</creationdate><title>The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase</title><author>Schuch, Benjamin ; Feigenbutz, Monika ; Makino, Debora L ; Falk, Sebastian ; Basquin, Claire ; Mitchell, Phil ; Conti, Elena</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6177-d5d36b0fb213212bcf5cf3504294cd5308e35cc2210c63878c469e61bf32e71c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Blotting, Western</topic><topic>Calorimetry</topic><topic>Chromatography, Gel</topic><topic>Crystallization</topic><topic>Crystallography</topic><topic>DEAD-box RNA Helicases - chemistry</topic><topic>DEAD-box RNA Helicases - metabolism</topic><topic>DNA-Binding Proteins - chemistry</topic><topic>DNA-Binding Proteins - metabolism</topic><topic>Electrophoresis, Polyacrylamide Gel</topic><topic>EMBO36</topic><topic>EMBO40</topic><topic>Enzymes</topic><topic>Escherichia coli</topic><topic>Exosome Multienzyme Ribonuclease Complex - chemistry</topic><topic>Exosome Multienzyme Ribonuclease Complex - metabolism</topic><topic>Fluorescence Polarization</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Multiprotein Complexes - chemistry</topic><topic>Multiprotein Complexes - metabolism</topic><topic>Mutation</topic><topic>nuclear exosome</topic><topic>Nuclear Proteins - chemistry</topic><topic>Nuclear Proteins - metabolism</topic><topic>Oligonucleotide Probes</topic><topic>Protein Conformation</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA degradation</topic><topic>RNA-Binding Proteins - chemistry</topic><topic>RNA-Binding Proteins - metabolism</topic><topic>Rosaniline Dyes</topic><topic>Saccharomyces cerevisiae - genetics</topic><topic>Saccharomyces cerevisiae Proteins - chemistry</topic><topic>Saccharomyces cerevisiae Proteins - metabolism</topic><topic>X-ray crystallography</topic><topic>yeast genetics</topic><topic>Yeasts</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schuch, Benjamin</creatorcontrib><creatorcontrib>Feigenbutz, Monika</creatorcontrib><creatorcontrib>Makino, Debora L</creatorcontrib><creatorcontrib>Falk, Sebastian</creatorcontrib><creatorcontrib>Basquin, Claire</creatorcontrib><creatorcontrib>Mitchell, Phil</creatorcontrib><creatorcontrib>Conti, Elena</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The EMBO journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Schuch, Benjamin</au><au>Feigenbutz, Monika</au><au>Makino, Debora L</au><au>Falk, Sebastian</au><au>Basquin, Claire</au><au>Mitchell, Phil</au><au>Conti, Elena</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase</atitle><jtitle>The EMBO journal</jtitle><stitle>EMBO J</stitle><addtitle>EMBO J</addtitle><date>2014-12-01</date><risdate>2014</risdate><volume>33</volume><issue>23</issue><spage>2829</spage><epage>2846</epage><pages>2829-2846</pages><issn>0261-4189</issn><eissn>1460-2075</eissn><coden>EMJODG</coden><abstract>The exosome is a conserved multi‐subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10‐subunit core complex of the exosome (Exo‐10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo‐10
in vitro
is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N‐terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N‐terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C‐terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.
Synopsis
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.
The N‐terminal domains of
S. cerevisiae
Rrp6 and Rrp47 form a highly intertwined structural unit.
The Rrp6–Rrp47 complex creates a composite and conserved surface groove that binds the N‐terminus of Mtr4 and recruits Mtr4 to the nuclear exosome.
Structure‐based mutations of conserved residues within Rrp6 and Mtr4 disrupt their interaction, result in 5.8S RNA processing defects
in vivo
and inhibit growth of strains expressing a C‐terminal GFP fusion of Mtr4.
Graphical Abstract
Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.</abstract><cop>London</cop><pub>Blackwell Publishing Ltd</pub><pmid>25319414</pmid><doi>10.15252/embj.201488757</doi><tpages>18</tpages><oa>free_for_read</oa></addata></record> |
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| issn | 0261-4189 1460-2075 |
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| source | Springer Nature OA Free Journals |
| subjects | Blotting, Western Calorimetry Chromatography, Gel Crystallization Crystallography DEAD-box RNA Helicases - chemistry DEAD-box RNA Helicases - metabolism DNA-Binding Proteins - chemistry DNA-Binding Proteins - metabolism Electrophoresis, Polyacrylamide Gel EMBO36 EMBO40 Enzymes Escherichia coli Exosome Multienzyme Ribonuclease Complex - chemistry Exosome Multienzyme Ribonuclease Complex - metabolism Fluorescence Polarization Models, Molecular Molecular biology Multiprotein Complexes - chemistry Multiprotein Complexes - metabolism Mutation nuclear exosome Nuclear Proteins - chemistry Nuclear Proteins - metabolism Oligonucleotide Probes Protein Conformation Ribonucleic acid RNA RNA degradation RNA-Binding Proteins - chemistry RNA-Binding Proteins - metabolism Rosaniline Dyes Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae Proteins - chemistry Saccharomyces cerevisiae Proteins - metabolism X-ray crystallography yeast genetics Yeasts |
| title | The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase |
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