Amino acids are not all initially attached to the same position on transfer RNA molecules.

Fraser, Thomas H.; Rich, Alexander

doi:10.1073/pnas.72.8.3044

Cited by 95 publications

(42 citation statements)

References 9 publications

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“…(ii) III contrast to the nine other members of class 11 tRNA synthetases, PheRS makes an exception in that it catalyzes the initial aminoacylation of the 2' hydroxyl of the terminal adcnosine of tRNA rather than the 3' hydroxyl [ 14,15]. The general distinction between 2'OH and 3'OH aminoacylation by class I and class I1 tRNA synthetases.…”

Section: Introductionmentioning

confidence: 99%

Cloning and sequence analysis of the phenylalanyl‐tRNA synthetase genes (pheST) from Thermus thermophilus

1992

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While crystals suil;lblc for X-ray diflixction ;m;llyscs urc uvailublc of phenylalunyl-tRNA symhctase (PhcRS) from the thermophilic bacurium T/rc~rr~ts rlr~~/,?t~p/ri/~r.s, ncithcr the primary slruciurc of its conslitucnt a andp subunits nor Ihc nuclcotidc scqucncc of the EorrcspondingpkS und plrt~T genes wcrc known. Using specilic oligonuclcolidus 01' conscrvcd phe.S regions th:ti wcrc adapted to the T. rharmoplrilus codon usage. WC idcntificd. cloned itnd subscqucntly scqucnccd the plrrST gcncs oT this bxtcrium. The sequences rcporkd hcrc will grcally nid in the ~hrce-dimensional struclurc dctcrmination or T.

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Section: Introductionmentioning

confidence: 99%

Cloning and sequence analysis of the phenylalanyl‐tRNA synthetase genes (pheST) from Thermus thermophilus

1992

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“…The tRNA synthetases closely related to the pol ␥ accessory subunit belong to the class II family of aminoacyl-tRNA synthetases, which differ from the class I enzymes in the aminoacylation site in the tRNA (3Ј OH versus 2Ј OH of the terminal ribose, with the exception of phenylalanyl-tRNA synthetase) (7,14,29) as well as in the structure of the active site of the enzyme. Class II enzymes contain a seven-stranded antiparallel ␤-sheet motif (18).…”

Section: Resultsmentioning

confidence: 99%

The Accessory Subunit of Xenopus laevis Mitochondrial DNA Polymerase γ Increases Processivity of the Catalytic Subunit of Human DNA Polymerase γ and Is Related to Class II Aminoacyl-tRNA Synthetases

Carrodeguas

Kobayashi

Lim

et al. 1999

Molecular and Cellular Biology

102

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Peptide sequences obtained from the accessory subunit of Xenopus laevis mitochondrial DNA (mtDNA) polymerase ␥ (pol ␥) were used to clone the cDNA encoding this protein. Amino-terminal sequencing of the mitochondrial protein indicated the presence of a 44-amino-acid mitochondrial targeting sequence, leaving a predicted mature protein with 419 amino acids and a molecular mass of 47.3 kDa. This protein is associated with the larger, catalytic subunit in preparations of active mtDNA polymerase. The small subunit exhibits homology to its human, mouse, and Drosophila counterparts. Interestingly, significant homology to glycyl-tRNA synthetases from prokaryotic organisms reveals a likely evolutionary relationship. Since attempts to produce an enzymatically active recombinant catalytic subunit of Xenopus DNA pol ␥ have not been successful, we tested the effects of adding the small subunit of the Xenopus enzyme to the catalytic subunit of human DNA pol ␥ purified from baculovirus-infected insect cells. These experiments provide the first functional evidence that the small subunit of DNA pol ␥ stimulates processive DNA synthesis by the human catalytic subunit under physiological salt conditions. Mitochondrial DNA (mtDNA) is replicated by a DNA polymerase, DNA polymerase ␥ (pol ␥), that is distinct from nuclear DNA polymerases ␣, ␤, ␦, ε, and . Since DNA pol ␥ represents only a small fraction of total cellular DNA polymerase, purification and characterization of the subunit composition of this enzyme have been difficult. Molecular cloning has contributed greatly to understanding the structure of DNA pol ␥ in different organisms. The catalytic subunits of DNA pol ␥ have been cloned for several organisms (6,16,17,27,34) and have been found to resemble family A of DNA polymerases, related to Escherichia coli DNA pol I. In Saccharomyces cerevisiae DNA pol ␥ is composed of a single polypeptide, while in Drosophila melanogaster DNA pol ␥ is comprised of two different polypeptides, a catalytic subunit of 125 kDa and an accessory subunit of 41 kDa (24, 33). The Drosophila subunits copurify and have been shown to interact, but the recombinant proteins have not yet been shown to be functional. The function of the small subunit, which we refer to as pol ␥B, is unknown. It has been proposed to influence the processivity of the catalytic subunit. Putative mammalian homologs of the Drosophila accessory subunit have been identified in sequence databases. One published purification scheme for human DNA pol ␥ suggested the existence of a small subunit (11), but the potential relationship between this polypeptide and Drosophila pol ␥B has not been established. Recently, the catalytic subunit of human DNA pol ␥ was expressed in an active form (10,19). Surprisingly, the recombinant catalytic subunit alone displayed most of the characteristics of the enzyme purified from human cells, which did not appear to contain a stoichiometric amount of a small subunit. Thus, it is not clear what role, if any, is played by putative human DNA pol ␥B.We hav...

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“…In Figure 2 (left half), each codon in the classical genetic code is colored according to the aminoacylation mechanism of its tRNA with 29OH codons colored in green and 39OH codons colored in red (Fraser and Rich 1975). This is equivalent to coloring according to the Class I/Class II partition, except for PheRS, which is an outlier in its own class ( Fig.…”

Section: Asymmetric Pattern In a Colored Codon Tablementioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

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Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here, an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

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Amino acids are not all initially attached to the same position on transfer RNA molecules.

Cited by 95 publications

References 9 publications

Cloning and sequence analysis of the phenylalanyl‐tRNA synthetase genes (pheST) from Thermus thermophilus

Cloning and sequence analysis of the phenylalanyl‐tRNA synthetase genes (pheST) from Thermus thermophilus

The Accessory Subunit of Xenopus laevis Mitochondrial DNA Polymerase γ Increases Processivity of the Catalytic Subunit of Human DNA Polymerase γ and Is Related to Class II Aminoacyl-tRNA Synthetases

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

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