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Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNAGly 'misediting paradox' is resolved by EF-Tu in the cell. Here, we show that DTD's active site architecture can efficiently edit mischarged Gly-tRNAAla species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error. Also, DTD knockout in AlaRS editing-defective background causes pronounced toxicity in Escherichia coli even at low-glycine levels which is alleviated by alanine supplementation. We further demonstrate that DTD positively selects the universally invariant tRNAAla-specific G3•U70. Moreover, DTD's activity on non-cognate Gly-tRNAAla is conserved across all bacteria and eukaryotes, suggesting DTD's key cellular role as a glycine deacylator. Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance.
Pubmed ID: 28362257
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GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit. All the data presented in GenProtEC is made easily accessible to the users through downloadable flat files in text format. GenProtEC presents information on the functions of E.coli K-12 MG1655 gene products from several points of view. E.coli proteins as single modules have been grouped in sequence similarity. Using the power of group membership of proteins of similar function, open reading frames within any group can be assigned the general function. In addition, the presence of domains of known function within E.coli proteins has been determined. Domain content permits annotation of some functional information to otherwise totally unknown sequences. The rich classification of cellular roles, MultiFun, has been applied, underlining the fact that many gene products have more than one cellular role. Our annotation work includes multiple types of information: 1. Sequence similarity to orthologues as defined by Darwin (start and end of aligned region, identity, and PAM distance). 2. Resolution of fused proteins into modular units with independent functions. 3. Identification of sequence similar protein groups within E. coli that are clustered by transitive relationships. The sequence similarity is limited to PAM 200 and an alignment of at least 83 amino acids. 4. Updated literature references. 5. Classification of gene products by their gene type and by their cellular role(s). The MultiFun classification system for cellular roles is used to assign gene products to one or more roles. MultiFun has been converted to Gene Ontology terms. 6. Familes of proteins related by structure and biochemical reaction mechanisms (work in progress). 7. SCOP superfamily identification and location (e.g. binding site domains) for E. coli proteins.
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