4WJ3

Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa

Summary for 4WJ3

• Entry DOI: 10.2210/pdb4wj3/pdb
• Related: 4WJ4
• Descriptor: Glutamyl-tRNA(Gln) amidotransferase subunit A, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, Glutamyl-tRNA(Gln) amidotransferase subunit C, ... (5 entities in total)
• Functional Keywords: transamidosome, aminoacyl-trna synthetase, gatcab, trna, ligase-rna complex, ligase/rna
• Biological source: Pseudomonas aeruginosa PAO1; More
• Total number of polymer chains: 20
• Total formula weight: 825961.88

Authors

Suzuki, T.,Nakamura, A.,Kato, K.,Tanaka, I.,Yao, M. (deposition date: 2014-09-29, release date: 2014-12-31, Last modification date: 2024-10-09)

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 (3.705 Å)