Cytidines in tRNAs that are required intact by ATP/CTP:tRNA nucleotidyltransferases from<i>Escherichia coli</i>and<i>Saccharomyces cerevisiae</i>

Hegg, Lisa A.; Thurlow, David L.

doi:10.1093/nar/18.20.5975

Cited by 31 publications

(29 citation statements)

References 14 publications

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“…Val-34C consists of the acceptor-T stemloop of E. coli tRNA Val , which is the primary tRNA domain that is recognized by both classes in crystal structures (7,8), and is active for the stepwise nucleotide addition by both classes (20,21,24,25). Previous studies of addition to the 76 position of Val-34C were all performed with Mg 2+ .…”

Section: Resultsmentioning

confidence: 99%

Metal-Ion-Dependent Catalysis and Specificity of CCA-Adding Enzymes: A Comparison of Two Classes

Hou

Zhou

et al. 2005

Biochemistry

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The CCA-adding enzymes [ATP(CTP):tRNA nucleotidyl transferases] catalyze synthesis of the conserved and essential CCA sequence to the tRNA 3' end. These enzymes are divided into two classes of distinct structures that differ in the overall orientation of the head to tail domains. However, the catalytic core of the two classes is conserved and contains three carboxylates in a geometry commonly found in DNA and RNA polymerases that use the two-metal-ion mechanism for phosphoryl transfer. Two important aspects of the two-metal-ion mechanism are tested here for CCA enzymes: the dependence on metal ions for catalysis and for specificity of nucleotide addition. Using the archaeal Sulfolobus shibabae enzyme as an example of the class I, and the bacterial Escherichia coli enzyme as an example of the class II, we show that both enzymes depend on metal ions for catalysis, and that both use primarily Mg2+ and Mn2+ as the "productive" metal ions, but several other metal ions such as Ca2+ as the "nonproductive" metal ions. Of the two productive metal ions, Mg2+ specifically promotes synthesis of the correct CCA, whereas Mn2+ preferentially accelerates synthesis of the noncognate CCC and poly(C). Thus, despite evolution of structural diversity of two classes, both classes use metal ions to determine catalysis and specificity. These results provide critical insights into the catalytic mechanism of CCA synthesis to allow the two classes to be related to each other, and to members of the larger family of DNA and RNA polymerases.

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Section: Resultsmentioning

confidence: 99%

Metal-Ion-Dependent Catalysis and Specificity of CCA-Adding Enzymes: A Comparison of Two Classes

Hou

Zhou

et al. 2005

Biochemistry

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“…As deduced by a “damage-selection” approach involving limited chemical modification before 3′-adenylation, nucleotides in the T-loop and near the 3′-end are important for the recognition of TMV RNA by CCA-NTase (Hegg et al, 1990). Histidyl-TMV RNA is known to form a ternary complex with wheat germ eEF1A (Litvak et al, 1973), though the stability of the complex has not been determined.…”

Section: Trna Mimicry Of Valine- Histidine- and Tyrosine-specificmentioning

confidence: 99%

Role of tRNA-like structures in controlling plant virus replication

2009

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Transfer RNA-like structures (TLSs) that are sophisticated functional mimics of tRNAs are found at the 3′-termini of the genomes of a number of plant positive strand RNA viruses. Three natural aminoacylation identities are represented: valine, histidine, and tyrosine. Paralleling this variety in structure, the roles of TLSs vary widely between different viruses. For Turnip yellow mosaic virus, the TLS must be capable of valylation in order to support infectivity, major roles being the provision of translational enhancement and down-regulation of minus strand initiation. In contrast, valylation of the Peanut clump virus TLS is not essential. An intermediate situation seems to exist for Brome mosaic virus, whose RNAs 1 and 2, but not RNA3, need to be capable of tyrosylation to support infectivity. Other known roles for certain TLSs include (i) the recruitment of host CCA nucleotidyltransferase as a telomerase to maintain intact 3′ CCA termini, (ii) involvement in the encapsidation of viral RNAs, and (iii) presentation of minus strand promoter elements for replicase recognition. In the latter role, the promoter elements reside within the TLS but are not functionally dependent on tRNA mimicry. The phylogenetic distribution of TLSs indicates that their evolutionary history includes frequent horizontal exchange, as has been observed for protein-coding regions of plant positive strand RNA viruses.

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“…The CCA sequence at the 74-76 positions of the tRNA 39 end is important for many biological functions+ It provides the amino acid attachment site for tRNA to participate in protein synthesis+ It serves as the primer for initiation of replication by retroviruses (Maizels & Weiner, 1994)+ It is also important in the transport of eucaryotic tRNA from nucleus to cytoplasm as a checkpoint for tRNA maturity (Lund & Dahlberg, 1998)+ The synthesis and maintenance of the CCA sequence are carried out by the CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase], which catalyzes the addition of CMP, CMP, and AMP one at a time from the respective nucleotide triphosphate (Deutscher, 1982)+ This enzyme also adds the CCA sequence to the 39 end of viral RNAs that have the tRNA-like structures (Rao et al+, 1989;Hegg et al+, 1990;Giege, 1996)+ The CCAadding enzyme is present in all three domains of life, the eubacteria, the eucarya, and the archaea+ In organisms of eucarya and many archaea that do not encode the CCA sequence in tRNA genes, the CCAadding enzyme is responsible for the synthesis of CCA and thus it is essential (Aebi et al+, 1990)+ In organisms of eubacteria, such as Escherichia coli, that do encode the CCA sequence in tRNA genes, the CCA-adding enzyme is responsible for repairing damaged 39 ends by resynthesizing the CCA sequence+ The repair function of the CCA-adding enzyme is not essential (Zhu & Deutscher, 1987)+ E. coli strain that lacks the CCA enzyme is viable, albeit with a reduced growth rate+…”

Section: Introductionmentioning

confidence: 99%

Unusual synthesis by the Escherichia coli CCA-adding enzyme

Hou

2000

RNA

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The tRNA 39 end contains the conserved CCA sequence at the 74-76 positions. The CCA sequence is synthesized and maintained by the CCA-adding enzymes. The specificity of the Escherichia coli enzyme at each of the 74-76 positions was investigated using synthetic minihelix substrates that contain permuted 39 ends. Results here indicate that the enzyme has the ability to synthesize unusual 39 ends. When incubated with CTP alone, the enzyme catalyzed the addition of C74, C75, C76, and multiple Cs. Although the addition of C74 and C75 was as expected, that of C76 and multiple Cs was not. In particular, the addition of C76 generated CCC, which would have conflicted with the biological role of the enzyme. However, the presence of ATP prevented the synthesis of CCC and completely switched the specificity to CCA. The presence of ATP also had an inhibitory effect on the synthesis of multiple Cs. Thus, the E. coli CCA enzyme can be a poly(C) polymerase but its synthesis of poly(C) is regulated by the presence of ATP. These features led to a model of CCA synthesis that is independent of a nucleic acid template. The synthesis of poly(C) by the CCA-adding enzyme is reminiscent of that of poly(A) by poly(A) polymerase and it provides a functional rationale for the close sequence relationship between these two enzymes in the family of nucleotidyltransferases.

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Cytidines in tRNAs that are required intact by ATP/CTP:tRNA nucleotidyltransferases fromEscherichia coliandSaccharomyces cerevisiae

Cited by 31 publications

References 14 publications

Metal-Ion-Dependent Catalysis and Specificity of CCA-Adding Enzymes: A Comparison of Two Classes

Metal-Ion-Dependent Catalysis and Specificity of CCA-Adding Enzymes: A Comparison of Two Classes

Role of tRNA-like structures in controlling plant virus replication

Unusual synthesis by the Escherichia coli CCA-adding enzyme

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