4WJ4

Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid

Summary for 4WJ4

• Entry DOI: 10.2210/pdb4wj4/pdb
• Related: 4WJ3
• Descriptor: Aspartate--tRNA(Asp/Asn) ligase, 76mer-tRNA, ASPARTIC ACID (3 entities in total)
• Functional Keywords: non-discriminating asprs, trna, aminoacylation, ligase-rna complex, ligase/rna
• Biological source: Pseudomonas aeruginosa PAO1; More
• Total number of polymer chains: 2
• Total formula weight: 91916.28

Authors

Suzuki, T.,Nakamura, A.,Kato, K.,Tanaka, I.,Yao, M. (deposition date: 2014-09-29, release date: 2014-12-31, Last modification date: 2024-03-20)

Primary citation

Suzuki, T.,Nakamura, A.,Kato, K.,Soll, D.,Tanaka, I.,Sheppard, K.,Yao, M.
Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA, 112:382-387, 2015

PubMed Abstract: Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Å resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

PubMed: 25548166
DOI: 10.1073/pnas.1423314112

Experimental method

X-RAY DIFFRACTION (3.294 Å)