Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction
Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we...
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| Veröffentlicht in: | RNA (Cambridge) 2010-03, Vol.16 (3), p.474-481 |
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| creator | Qin, Haina Chen, Fading Huan, Xuelu Machida, Satoru Song, Jianxing Yuan, Y Adam |
| description | Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing. |
| doi_str_mv | 10.1261/rna.1965310 |
| format | Article |
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However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. 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These data suggest a potential functional role of the Arabidopsis DUF283 domain in target selection in small RNA processing.</description><subject>Arabidopsis - chemistry</subject><subject>Binding Sites</subject><subject>Models, Molecular</subject><subject>Nuclear Magnetic Resonance, Biomolecular</subject><subject>Protein Structure, Tertiary</subject><subject>Ribonuclease III - chemistry</subject><subject>RNA, Double-Stranded - chemistry</subject><issn>1355-8382</issn><issn>1469-9001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkU9rFTEUxYMotlZX7iU7F2Vq_k1mZiM8Xq0KDwW163AnuWkj85Jnkin4LfzIRvosurk3yflx7g2HkJecXXCh-Zsc4YJPupecPSKnXOmpmxjjj9tZ9n03ylGckGelfG-PsslPyYlgnOmpl6fk19eaV1vXjDR5Wm-RbjLMwaVDCaXdYQkQgV5ud4peXl-JUVKX9hAizXiHsBQKNKZooZVgYWnqOi_YlZohOnT0y6dNN4foQryhPi2ulUwPOVUMsTt2GmLFDLaGFJ-TJ77Z4otjPyPXV---bT90u8_vP243u84qpWsH1oH2Xlmn_TiqwSpsH5VMD2KecFZaKugVY2KcBDaw7wG8GoZJCz8A0_KMvL33PazzHp3F2DZezCGHPeSfJkEw_ysx3JqbdGfEKMTERTN4fTTI6ceKpZp9KBaXBSKmtZhBSj2Mg2KNPL8nbU6lZPQPUzgzfyI0LUJzjLDRr_5d7IH9m5n8DRzXmgM</recordid><startdate>20100301</startdate><enddate>20100301</enddate><creator>Qin, Haina</creator><creator>Chen, Fading</creator><creator>Huan, Xuelu</creator><creator>Machida, Satoru</creator><creator>Song, Jianxing</creator><creator>Yuan, Y Adam</creator><general>Cold Spring Harbor Laboratory Press</general><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20100301</creationdate><title>Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction</title><author>Qin, Haina ; Chen, Fading ; Huan, Xuelu ; Machida, Satoru ; Song, Jianxing ; Yuan, Y Adam</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c446t-acda6ff4cd6f8847c4e83830672b9eb4634a54002892e6ff55aaf477962f7a063</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Arabidopsis - chemistry</topic><topic>Binding Sites</topic><topic>Models, Molecular</topic><topic>Nuclear Magnetic Resonance, Biomolecular</topic><topic>Protein Structure, Tertiary</topic><topic>Ribonuclease III - chemistry</topic><topic>RNA, Double-Stranded - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Qin, Haina</creatorcontrib><creatorcontrib>Chen, Fading</creatorcontrib><creatorcontrib>Huan, Xuelu</creatorcontrib><creatorcontrib>Machida, Satoru</creatorcontrib><creatorcontrib>Song, Jianxing</creatorcontrib><creatorcontrib>Yuan, Y Adam</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>RNA (Cambridge)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qin, Haina</au><au>Chen, Fading</au><au>Huan, Xuelu</au><au>Machida, Satoru</au><au>Song, Jianxing</au><au>Yuan, Y Adam</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction</atitle><jtitle>RNA (Cambridge)</jtitle><addtitle>RNA</addtitle><date>2010-03-01</date><risdate>2010</risdate><volume>16</volume><issue>3</issue><spage>474</spage><epage>481</epage><pages>474-481</pages><issn>1355-8382</issn><eissn>1469-9001</eissn><abstract>Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF283 domain of DCL4 displays weak dsRNA binding affinity and specifically binds to double-stranded RNA-binding domain 1 (dsRBD1) of Arabidopsis DRB4, whereas the DUF283 domain of DCL1 specifically binds to dsRBD2 of Arabidopsis HYL1. 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| subjects | Arabidopsis - chemistry Binding Sites Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Structure, Tertiary Ribonuclease III - chemistry RNA, Double-Stranded - chemistry |
| title | Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction |
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