Crystal Structure of Archaeosine tRNA-guanine Transglycosylase

Ishitani, Ryuichiro; Nureki, Osamu; Fukai, Shuya; Kijimoto, Teiya; Nameki, Nobukazu; Watanabe, Masakatsu; Kondo, Hisao; Sekine, Mitsuo; Okada, Norihiro; Nishimura, Susumu; Yokoyama, Shigeyuki

doi:10.1016/s0022-2836(02)00090-6

Cited by 61 publications

(71 citation statements)

References 47 publications

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“…Proteins that contain PUA domains function in enzymatic RNA modification like pseudouridine synthases or tRNA modifying enzymes (Cerrudo et al 2014). The crystal structure of the Pyrococcus horikoshii archaeosine tRNA-Guanine transglycosylase (ArcTGT) shows that the PUA domain directly contacts the RNA substrate and contributes to the specificity of the protein (Ishitani et al 2002). tRNA binding by the ArcTGT involved direct contact to the CCA via a specific surface formed by the PUA domain.…”

Section: Methylation Of Trnamentioning

confidence: 99%

NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs

Haag

Warda

Kretschmer

et al. 2015

RNA

161

151

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Many cellular RNAs require modification of specific residues for their biogenesis, structure, and function. 5-methylcytosine (m 5 C) is a common chemical modification in DNA and RNA but in contrast to the DNA modifying enzymes, only little is known about the methyltransferases that establish m 5 C modifications in RNA. The putative RNA methyltransferase NSUN6 belongs to the family of Nol1/Nop2/SUN domain (NSUN) proteins, but so far its cellular function has remained unknown. To reveal the target spectrum of human NSUN6, we applied UV crosslinking and analysis of cDNA (CRAC) as well as chemical crosslinking with 5-azacytidine. We found that human NSUN6 is associated with tRNAs and acts as a tRNA methyltransferase. Furthermore, we uncovered tRNA Cys and tRNA Thr as RNA substrates of NSUN6 and identified the cytosine C72 at the 3 ′ end of the tRNA acceptor stem as the target nucleoside. Interestingly, target recognition in vitro depends on the presence of the 3 ′ -CCA tail. Together with the finding that NSUN6 localizes to the cytoplasm and largely colocalizes with marker proteins for the Golgi apparatus and pericentriolar matrix, our data suggest that NSUN6 modifies tRNAs in a late step in their biogenesis.

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Section: Methylation Of Trnamentioning

confidence: 99%

NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs

Haag

Warda

Kretschmer

et al. 2015

RNA

161

151

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“…The unique FSF (SCOP superfamily d.17.6) is found in an enzyme involved in the synthesis of archaeosine, a modified base (7-formamidino-7-deazaguanosine) found exclusively in the Archaea (34). The SCOP entry has been assigned to a fold level that includes six superfamilies, including cystatin-like folds.…”

Section: Eukaryamentioning

confidence: 99%

Phylogeny determined by protein domain content

Yang

Doolittle

Bourne

2005

Proc. Natl. Acad. Sci. U.S.A.

204

137

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A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size (number of considered folds), small-genome taxa were mostly grouped with their full-sized counterparts. Although not every organism appears exactly at its classical phylogenetic position in these trees, the agreement appears comparable with the efforts of others by using sophisticated sequence analysis and͞or combinations of gene content and gene order. During the course of the study, it emerged that there is a core set of Ϸ50 folds that is found in all 174 genomes and a single fold diagnostic of all Archaea.fold superfamily T he advent of the era of complete genome sequences has led to a variety of approaches for determining the evolutionary history of organisms over and beyond the comparison of the sequences themselves (1-4), including the use of such features as concatenated protein sequences (5, 6), gene content (1-3, 7), gene order (8-10), and the distribution of structural folds (11-15). Such efforts have continued even though there are those who feel the construction of a unified phylogeny is a hopeless task, horizontal gene transfers having been too pervasive to allow a singular depiction (16). In this vein, it is fair to say that the resulting phylogenies have not been entirely consistent between one method and another, and certainly none on its own has resulted in a wholly satisfactory classification. Attempts to filter out anomalies (17) or the use of combinations of various approaches (9, 10) have been more satisfactory, but incongruities remain.The principal goal of these endeavors is to generate a phylogeny that best represents the evolutionary histories of the taxa represented, and that resolves previous incongruities. It is generally agreed that three major forces are at work in modifying the genetic information in any genome: (i) expansion (gene duplication), (ii) deletion (gene loss), and (iii) exchange (horizontal transfer) (18)(19)(20)(21)(22). Additionally, there must be some degree of de novo ''gene genesis,'' the concoction of new genes by various means (23). The challenge is to find the level of informational bundling that best accounts for this combination of events.Here we report a simple scheme that uses a structural attribute, the protein domain content, as the principal determinant of relatedness. In particular, we have focused on the fold superfamily level (FSF) as opposed to the fold grouping itself that has been used by many other workers in the past (11-15). It is a subtle but critical distinction (14). The mere presence or absence of an FSF in a genome, as opposed to its overall abundance, was ...

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“…It has been shown that 7-cyano-7-deazaguanine (preQ 0 ) is an intermediate in the pathway and is inserted into tRNA by a tRNA-guanine transglycosylase (TGT, EC 2.4.2.29) encoded by the tgtA gene (Bai et al 2000, Watanabe et al 2001). This enzyme has been extensively investigated biochemically and structurally (Ishitani et al 2002), but no deletion mutant has ever been constructed in any archaeal organism. By deleting the corresponding HVO_2001 gene, we will address the essentiality of a protein family that is found in most archaeal genomes sequenced thus far.…”

Section: Introductionmentioning

confidence: 99%

A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes

Yacoubi

Phillips

Blaby‐Haas

et al. 2009

Archaea

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SummaryIn part due to the existence of simple methods for its cultivation and genetic manipulation, Haloferax volcanii is a major archaeal model organism. It is the only archaeon for which the whole set of post-transcriptionally modified tRNAs has been sequenced, allowing for an in silico prediction of all RNA modification genes present in the organism. One approach to check these predictions experimentally is via the construction of targeted gene deletion mutants. Toward this goal, an integrative "Gateway vector" that allows gene deletion in H. volcanii uracil auxotrophs was constructed. The vector was used to delete three predicted tRNA modification genes: HVO_2001 (encoding an archaeal transglycosyl tranferase or arcTGT), which is involved in archeosine biosynthesis; HVO_2348 (encoding a newly discovered GTP cyclohydrolase I), which catalyzes the first step common to archaeosine and folate biosynthesis; and HVO_2736 (encoding a member of the COG1444 family), which is involved in N 4 -acetylcytidine (ac 4 C) formation. Preliminary phenotypic analysis of the deletion mutants was conducted, and confirmed all three predictions.

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Crystal Structure of Archaeosine tRNA-guanine Transglycosylase

Cited by 61 publications

References 47 publications

NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs

NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs

Phylogeny determined by protein domain content

A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes

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Crystal Structure of Archaeosine tRNA-guanine Transglycosylase

Cited by 61 publications

References 47 publications

NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs

NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs

Phylogeny determined by protein domain content

A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes

Contact Info

Product

Resources

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NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs

NSUN6 is a human RNA methyltransferase that catalyzes formation of m⁵C72 in specific tRNAs