Crystal Structure of a Cbf5-Nop10-Gar1 Complex and Implications in RNA-Guided Pseudouridylation and Dyskeratosis Congenita

Rashid, Rumana; Liang, Bo; Baker, Daniel L.; Youssef, Osama; He, Yang; Phipps, Kathleen R.; Terns, Rebecca M.; Terns, Michael P.; Li, Hong

doi:10.1016/j.molcel.2005.11.017

Cited by 147 publications

(247 citation statements)

References 77 publications

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“…This is consistent with the literature because, despite the low sequence similarity between them, dyskerin shows strong structural similarity to TruB (bacterial pseudouridine synthase) and for that reason is considered to be the pseudouridine synthase of H/ACA small nucleolar RNPs [67,68]. However, these proteins have some differences, the PUA domain of TruB makes nonsequence-specific contacts with the acceptor stem of tRNA, the PUA domain of dyskerin is considerably larger than that of TruB, and the angle formed between the PUA domain and the core Ψ synthase fold extends the active site cleft in the other direction [30].…”

Section: Comparative Analysis Of the Pua Domain Between The Differentmentioning

confidence: 99%

Protein universe containing a PUA RNA‐binding domain

2013

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Here, we review current knowledge about pseudouridine synthase and archaeosine transglycosylase (PUA)‐domain‐containing proteins to illustrate progress in this field. A methodological analysis of the literature about the topic was carried out, together with a ‘qualitative comparative analysis’ to give a more comprehensive review. Bioinformatics methods for whole‐protein or protein‐domain identification are commonly based on pairwise protein sequence comparisons; we added comparison of structures to detect the whole universe of proteins containing the PUA domain. We present an update of proteins having this domain, focusing on the specific proteins present in Homo sapiens (dyskerin, MCT1, Nip7, eIF2D and Nsun6), and explore the existence of these in other species. We also analyze the phylogenetic distribution of the PUA domain in different species and proteins. Finally, we performed a structural comparison of the PUA domain through data mining of structural databases, determining a conserved structural motif, despite the differences in the sequence, even among eukaryotes, archaea and bacteria. All data discussed in this review, both bibliographic and analytical, corroborate the functional importance of the PUA domain in RNA‐binding proteins.

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Section: Comparative Analysis Of the Pua Domain Between The Differentmentioning

confidence: 99%

Protein universe containing a PUA RNA‐binding domain

2013

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“…To address this question, a great deal of efforts have been expended to solve the crystal structures of archaeal box H/ACA snRNP complexes. As a result, the structures of various forms, from the initial complex of three core proteins to a complete, substrate-bound box H/ACA RNP, have been solved (Li and Ye, 2006;Manival et al, 2006;Rashid et al, 2006;Liang et al, 2007;Duan et al, 2009;Liang et al, 2009). A detailed picture of how this most complex pseudouridylase modifies its substrate has now become available.…”

Section: Spliceosomal Snrna Pseudouridylation Is Induced At Novel Sitmentioning

confidence: 99%

Pseudouridines in spliceosomal snRNAs

2011

Protein Cell

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Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.

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“…Conversely, the exchange of the other core proteins could reflect a possible rearrangement or breathing of the complex during catalysis. For example, recent crystal structures of partial archaeal H/ACA protein complexes demonstrate how NOP10 brackets the catalytic domain of NAP57 (Hamma et al 2005;Manival et al 2006;Rashid et al 2006). During catalysis this NOP10-NAP57 interaction may need to be loosened to allow access to and/or release of substrate RNAs.…”

Section: Protein Dynamics Of H/aca Rnpsmentioning

confidence: 99%

Dynamic association and localization of human H/ACA RNP proteins

Kittur¹,

Darzacq²,

Roy³

et al. 2006

RNA

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Mammalian H/ACA RNPs are essential for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. To form mature RNA-protein complexes, one H/ACA RNA associates with four core proteins. In the cell, this process is assisted by at least one nuclear assembly factor, NAF1. Here we report several unanticipated dynamic aspects of H/ACA RNP proteins. First, when overexpressed, NAF1 delocalizes to the cytoplasm. However, its nucleocytoplasmic shuttling properties remain unaffected. These observations demonstrate a subtle equilibrium between NAF1 expression levels and the availability of NAF1 nuclear binding sites. Second, although NAF1 is excluded from mature RNPs in nucleoli and Cajal bodies, NAF1 associates with mature H/ACA RNA in cell lysates. This association occurs post-lysis because it is observed even when NAF1 and the H/ACA RNA are expressed in separate cells. This documents a protein-RNP association in cell lysates that is absent from intact cells. Third, in similar experiments, all H/ACA core proteins, except NAP57, exchange with their exogenous counterparts, portraying an unexpected dynamic picture of H/ACA RNPs. Finally, the irreversible association of only NAP57 with H/ACA RNA and the conundrum that only NAP57 is mutated in X-linked dyskeratosis congenita (even though most core proteins are required for maintaining H/ACA RNAs) may be more than a coincidence.

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Crystal Structure of a Cbf5-Nop10-Gar1 Complex and Implications in RNA-Guided Pseudouridylation and Dyskeratosis Congenita

Cited by 147 publications

References 77 publications

Protein universe containing a PUA RNA‐binding domain

Protein universe containing a PUA RNA‐binding domain

Pseudouridines in spliceosomal snRNAs

Dynamic association and localization of human H/ACA RNP proteins

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