Specificity and catalysis hardwired at the RNA–protein interface in a translational proofreading enzyme

Sadeem Ahmad, Sowndarya Muthukumar, Santosh Kumar Kuncha, Satya Brata Routh, Antony S.K. Yerabham, Tanweer Hussain, Venu Kamarthapu, Shobha P Kruparani and Rajan Sankaranarayanan ()
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Sadeem Ahmad: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Sowndarya Muthukumar: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Santosh Kumar Kuncha: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Satya Brata Routh: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Antony S.K. Yerabham: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Tanweer Hussain: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Venu Kamarthapu: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Shobha P Kruparani: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research
Rajan Sankaranarayanan: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research

Nature Communications, 2015, vol. 6, issue 1, 1-12

Abstract: Abstract Proofreading modules of aminoacyl-tRNA synthetases are responsible for enforcing a high fidelity during translation of the genetic code. They use strategically positioned side chains for specifically targeting incorrect aminoacyl-tRNAs. Here, we show that a unique proofreading module possessing a D-aminoacyl-tRNA deacylase fold does not use side chains for imparting specificity or for catalysis, the two hallmark activities of enzymes. We show, using three distinct archaea, that a side-chain-stripped recognition site is fully capable of solving a subtle discrimination problem. While biochemical probing establishes that RNA plays the catalytic role, mechanistic insights from multiple high-resolution snapshots reveal that differential remodelling of the catalytic core at the RNA–peptide interface provides the determinants for correct proofreading activity. The functional crosstalk between RNA and protein elucidated here suggests how primordial enzyme functions could have emerged on RNA–peptide scaffolds before recruitment of specific side chains.

Date: 2015
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DOI: 10.1038/ncomms8552

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