Annotation inferences using phylogenetic trees
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli.
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Matched transductants distinguish tRNA m5U presence from broader genetic effects.
"Matched pairs of transductant strains differing by the presence of absence of 5-methyluridine (ribothymidine) (m5U) in their transfer ribonucleic acid (tRNA) were used to study the function of this modified nucleoside in Escherichia coli."
Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.
Protein abundance profiling of the Escherichia coli cytosol.
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The experiment measured a cytosolic E. coli protein fraction; the target-specific supplementary row remains uninspected.
"we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100."
The methyltransferase TrmA facilitates tRNA folding through interaction with its RNA-binding domain.
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TrmA assists tRNA folding without requiring its methyltransferase catalytic activity.
"We directly show that TrmA enhances tRNA folding in vitro independent of its catalytic activity."
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The RNA-binding-domain residues F106/H125 contribute directly to tRNA recognition.
"We identify two conserved residues, F106 and H125, in the RNA-binding domain of TrmA, which interact with the tRNA elbow and are critical for tRNA binding."
Isolation and chracterization of m5U-methyltransferase from Escherichia coli.
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Purified target enzyme supports tRNA methylation.
"The tRNA-modifying enzyme, S-adenosylmethionine: tRNA (uridine-5)-methyltransferase, has been purified essentially to homogeneity from an Escherichia coli strain containing an elevated level of this enzyme."
The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3'-end fragment of 16 S rRNA.
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TrmA associates with tRNA and a 16S rRNA fragment.
"After sequencing and Southern blot analyses, the RNA was identified to be a subset of undermodified tRNA species as well as the 3' terminus of 16 S rRNA."
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The covalent RNA complex is not ribosome-associated.
"However, the complex is not associated with the ribosome and the covalently bound RNA does not affect the tRNA methylating activity of the enzyme."
RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA.
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Loss of TrmA removes tmRNA m5U, establishing a second RNA substrate class.
"The evidence comes from the lack of m (5)U in purified tmRNA or TLD variants recovered from an Escherichia coli mutant strain deleted of the trmA gene."
Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.
Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity.