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Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea
- Source :
- EMBO Journal, EMBO Journal, EMBO Press, 2006, 25 (17), pp.4152-62. ⟨10.1038/sj.emboj.7601278⟩
- Publication Year :
- 2006
- Publisher :
- HAL CCSD, 2006.
-
Abstract
- International audience; To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation.
- Subjects :
- Models, Molecular
Pyrococcus abyssi
MESH: Amino Acid Sequence
RNA, Transfer, Amino Acyl
01 natural sciences
chemistry.chemical_compound
MESH: Protein Structure, Tertiary
Protein structure
Transfer RNA Aminoacylation
MESH: Pyrococcus abyssi
MESH: Threonine-tRNA Ligase
0303 health sciences
biology
General Neuroscience
Stereoisomerism
Translation (biology)
MESH: Archaeal Proteins
Biochemistry
RNA editing
Transfer RNA
MESH: Models, Molecular
Archaeal Proteins
Molecular Sequence Data
010402 general chemistry
Article
General Biochemistry, Genetics and Molecular Biology
03 medical and health sciences
MESH: RNA, Transfer, Amino Acyl
Threonine-tRNA Ligase
MESH: Lysine
MESH: RNA Editing
Amino Acid Sequence
Molecular Biology
030304 developmental biology
Aminoacyl-tRNA
Binding Sites
MESH: Molecular Sequence Data
General Immunology and Microbiology
Aminoacyl tRNA synthetase
Lysine
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology
biology.organism_classification
MESH: Stereoisomerism
Protein Structure, Tertiary
0104 chemical sciences
MESH: Transfer RNA Aminoacylation
chemistry
MESH: Binding Sites
RNA Editing
Subjects
Details
- Language :
- English
- ISSN :
- 02614189 and 14602075
- Database :
- OpenAIRE
- Journal :
- EMBO Journal, EMBO Journal, EMBO Press, 2006, 25 (17), pp.4152-62. ⟨10.1038/sj.emboj.7601278⟩
- Accession number :
- edsair.doi.dedup.....4005377182cd505eea68f9014cc9e6f5