4NBI

D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution

Summary for 4NBI

• Entry DOI: 10.2210/pdb4nbi/pdb
• Related: 4NBJ
• Descriptor: D-tyrosyl-tRNA(Tyr) deacylase, 3'-deoxy-3'-(D-tyrosylamino)adenosine, TRIETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: dtd, deacylase, dtd-like, hydrolase
• Biological source: Plasmodium falciparum
• Cellular location: Cytoplasm : Q8IIS0
• Total number of polymer chains: 2
• Total formula weight: 39475.20

Authors

Ahmad, S.,Routh, S.B.,Kamarthapu, V.,Sankaranarayanan, R. (deposition date: 2013-10-23, release date: 2013-12-18, Last modification date: 2023-11-08)

Primary citation

Ahmad, S.,Routh, S.B.,Kamarthapu, V.,Chalissery, J.,Muthukumar, S.,Hussain, T.,Kruparani, S.P.,Deshmukh, M.V.,Sankaranarayanan, R.
Mechanism of chiral proofreading during translation of the genetic code.
Elife, 2:e01519-e01519, 2013

PubMed Abstract: The biological macromolecular world is homochiral and effective enforcement and perpetuation of this homochirality is essential for cell survival. In this study, we present the mechanistic basis of a configuration-specific enzyme that selectively removes D-amino acids erroneously coupled to tRNAs. The crystal structure of dimeric D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with a substrate-mimicking analog shows how it uses an invariant 'cross-subunit' Gly-cisPro dipeptide to capture the chiral centre of incoming D-aminoacyl-tRNA. While no protein residues are directly involved in catalysis, the unique side chain-independent mode of substrate recognition provides a clear explanation for DTD's ability to act on multiple D-amino acids. The strict chiral specificity elegantly explains how the enriched cellular pool of L-aminoacyl-tRNAs escapes this proofreading step. The study thus provides insights into a fundamental enantioselection process and elucidates a chiral enforcement mechanism with a crucial role in preventing D-amino acid infiltration during the evolution of translational apparatus. DOI: http://dx.doi.org/10.7554/eLife.01519.001.

PubMed: 24302572
DOI: 10.7554/eLife.01519

Experimental method

X-RAY DIFFRACTION (1.86 Å)