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A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate.

ABSTRACT: The structural organization and functionality of aminoacyl-tRNA synthetases have been expanded through polypeptide additions to their core aminoacylation domain. We have identified a novel domain appended to the methionyl-tRNA synthetase (MetRS) of the intracellular pathogen Mycoplasma penetrans. Sequence analysis of this N-terminal region suggests the appended domain is an aminotransferase, which we demonstrate here. The aminotransferase domain of MpMetRS is capable of generating methionine from its ?-keto acid analog, 2-keto-4-methylthiobutyrate (KMTB). The methionine thus produced can be subsequently attached to cognate tRNA^Met in the MpMetRS aminoacylation domain. Genomic erosion in the Mycoplasma species has impaired many canonical biosynthetic pathways, causing them to rely on their host for numerous metabolites. It is still unclear if this bifunctional MetRS is a key part of pathogen life cycle or is a neutral consequence of the reductive evolution experienced by Mycoplasma species.

SUBMITTER: Muraski M

PROVIDER: S-EPMC7694997 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate.

Muraski Marc M Nilsson Emil E Weekley Benjamin B Sharma Sandhya Bharti SB Alexander Rebecca W RW

Genes 20201107 11

The structural organization and functionality of aminoacyl-tRNA synthetases have been expanded through polypeptide additions to their core aminoacylation domain. We have identified a novel domain appended to the methionyl-tRNA synthetase (MetRS) of the intracellular pathogen <i>Mycoplasma penetrans</i>. Sequence analysis of this N-terminal region suggests the appended domain is an aminotransferase, which we demonstrate here. The aminotransferase domain of MpMetRS is capable of generating methion ...[more]

PMID: 33171705

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Project description:MotivationSimilarities in core residue packing provide evidence for divergence or convergence not reported using other methods.ResultsWe apply a new method for rapid structure comparison based on Simplicial Neighborhood Analysis of Protein Packing (SNAPP) to the diverse structural classification of proteins (SCOP) alpha/beta-class of protein folds. The procedure identifies inter-residue packing motifs shared by protein pairs from different folds. A threshold of 0.67 A RMSD for all atoms of corresponding residues ensures inclusion of only highly significant similarities comparable with those observed for identical catalytic residues in homologues. Many tertiary packing motifs are shared among the three classical Rossmannoid folds, as well as thousands of other motifs that occur in at least two distinct folds. Merging of neighboring packing motifs facilitated recognition of larger, recurrent substructures or cores. The anti-codon-binding domain of an archeal aminoacyl-tRNA synthetase (aaRS) was discovered to possess a packed core in which eight identical amino acid residues are within 0.55 A RMSD of the comparable structure in the FixJ receiver, a member of the Rossmannoid family that also includes the CheY signaling protein and flavodoxin-like proteins. Further investigation identified close variants of this core in five other Rossmannoid folds, including a functionally relevant core in Class Ia aminoacyl-tRNA synthetases. Although it is possible that the two essentially identical cores in the ProRS anti-codon-binding domain and the FixJ receiver converged to the same structure, the consensus core obtained from the structural and sequence alignments suggests that all the implicated protein folds descended from a simpler ancestral protein in which this core provided nucleotide binding and proto-allosteric functions.AvailabilityPrograms are available at http://staff.vbi.vt.edu/cammer/snapp/download/ImplementationPrograms were written in Perl and c and run under Linux.Contactcammer@vbi.vt.edu.

Dataset Information

A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate.

Publications

A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate.

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