Unveiling substrate RNA binding to H/ACA RNPs: one side fits all

Current Opinion in Structural Biology

Volumn 18, Issue 1, 2008, Pages 78-85

  Li, Hong ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORE PROTEIN;

CHEMICAL ANALYSIS; ENZYME ACTIVATION; HUMAN; PRIORITY JOURNAL; REVIEW; RNA BINDING; RNA STRUCTURE;

ANIMALS; BINDING SITES; HUMANS; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RIBONUCLEOPROTEINS, SMALL NUCLEOLAR; RNA, SMALL NUCLEOLAR;

EID: 39149123489     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.11.004     Document Type: Review

References (46)

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24. •].
25. •] are the first to describe in vitro reconstitution of pseudouridylation activity from recombinant archaeal components. By using gel mobility shift assays, both works demonstrated the dominant role of Cbf5 in binding the guide RNA as well as the requirement for both domains of Cbf5. In addition, both works dissected the requirement of accessory proteins and the elements of the guide RNA for pseudouridylation activity. These works concluded that L7Ae and Nop10 are required for and Gar1 greatly enhances pseudouridylation activity.
26. •].
27. •].
28. ••]), suggesting that H/ACA protein core complexes remain largely rigid throughout the assembly process.
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35. Wang C., and Meier U.T. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. EMBO J 23 (2004) 1857-1867. This work reports the first attempt of reconstituting mammalian H/ACA RNPs by using in vitro transcribed and translated components. The basic conclusion from this work is similar to that with archaeal components with the exception that NH2P in fact binds to NOP10 instead of to RNA. This work also reports a possible close encounter of Gar1 with the target uridine on the basis of cross-linking studies.
36. Li L., and Ye K. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature 443 (2006) 302-307. This is the first report of a H/ACA RNP structure. A crystal structure of all proteins bound with a guide RNA was determined to 2.3 Å. The key findings include that the 3′ ACA tail is anchored by the PUA domain in a sequence-dependent manner, and the upper stem is anchored by a composite binding site formed by Cbf5, Nop10, and L7Ae.
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39. Jin H., Loria J.P., and Moore P.B. Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA. Mol Cell 26 (2007) 205-215. This is a thorough structural and biophysical study on substrate RNA binding to an isolated model H/ACA guide RNA derived from the 5′ portion of the human U65 snoRNA. The key conclusion is that the substrate RNA can bind to the pseudouridine pocket without the aid of proteins and in a simple unthreaded fashion. This guide-substrate RNA complex is unusual and contains five, rather than the normally two, unpaired nucleotides in the pseudouridine pocket. Detailed characterization of binding affinities at varying magnesium concentrations suggests the involvement of metal ions in the formation of the guide-substrate RNA complex. The NMR structure of the RNA complex resembles the shape of 'Ω', which leads to the term 'Ω-motif'.
40. ••], the U65 3′ RNA complex has a canonical secondary structure. The substrate strand is described as U-shaped.
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43. ••]), the upper stem of the guide RNA displays a large orientational difference. This difference was attributed to the lack of L7Ae and forms the structural basis for L7Ae-dependent substrate RNA placement. A fluorescence assay sensitive to the conformation of the nucleotide immediate 3′ of the target uridine provided strong evidence consistent with the proposed model based on the structural studies.
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