4RRF

Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with L-Ser3AA

Summary for 4RRF

• Entry DOI: 10.2210/pdb4rrf/pdb
• Related: 4RR6 4RR7 4RR8 4RR9 4RRA 4RRB 4RRC 4RRD 4RRG 4RRH 4RRI 4RRJ 4RRK 4RRL 4RRM 4RRQ 4RRR
• Descriptor: Threonine--tRNA ligase, SERINE-3'-AMINOADENOSINE, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: dtd-like fold, proofreading, ligase
• Biological source: Methanocaldococcus jannaschii
• Cellular location: Cytoplasm : Q58597
• Total number of polymer chains: 6
• Total formula weight: 97911.88

Authors

Ahmad, S.,Yerabham, A.S.K.,Kamarthapu, V.,Sankaranarayanan, R. (deposition date: 2014-11-06, release date: 2015-07-15, Last modification date: 2024-02-28)

Primary citation

Ahmad, S.,Muthukumar, S.,Kuncha, S.K.,Routh, S.B.,Yerabham, A.S.,Hussain, T.,Kamarthapu, V.,Kruparani, S.P.,Sankaranarayanan, R.
Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Nat Commun, 6:7552-7552, 2015

PubMed 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.

PubMed: 26113036
DOI: 10.1038/ncomms8552

Experimental method

X-RAY DIFFRACTION (1.7 Å)