3H0L

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus

Summary for 3H0L

• Entry DOI: 10.2210/pdb3h0l/pdb
• Related: 2DF4 2F2A 2G5H 2G5I 2GI3 3H0M
• Descriptor: Glutamyl-tRNA(Gln) amidotransferase subunit A, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, Glutamyl-tRNA(Gln) amidotransferase subunit C, ... (7 entities in total)
• Functional Keywords: multi protein complex, ligase, protein biosynthesis
• Biological source: Aquifex aeolicus; More
• Total number of polymer chains: 24
• Total formula weight: 964763.74

Authors

Wu, J.,Bu, W.,Sheppard, K.,Kitabatake, M.,Soll, D.,Smith, J.L. (deposition date: 2009-04-09, release date: 2009-07-21, Last modification date: 2024-11-20)

Primary citation

Wu, J.,Bu, W.,Sheppard, K.,Kitabatake, M.,Kwon, S.T.,Soll, D.,Smith, J.L.
Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme
J.Mol.Biol., 391:703-716, 2009

PubMed Abstract: Many bacteria form Gln-tRNA(Gln) and Asn-tRNA(Asn) by conversion of the misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) species catalyzed by the GatCAB amidotransferase in the presence of ATP and an amide donor (glutamine or asparagine). Here, we report the crystal structures of GatCAB from the hyperthermophilic bacterium Aquifex aeolicus, complexed with glutamine, asparagine, aspartate, ADP, or ATP. In contrast to the Staphylococcus aureus GatCAB, the A. aeolicus enzyme formed acyl-enzyme intermediates with either glutamine or asparagine, in line with the equally facile use by the amidotransferase of these amino acids as amide donors in the transamidation reaction. A water-filled ammonia channel is open throughout the length of the A. aeolicus GatCAB from the GatA active site to the synthetase catalytic pocket in the B-subunit. A non-catalytic Zn(2+) site in the A. aeolicus GatB stabilizes subunit contacts and the ammonia channel. Judged from sequence conservation in the known GatCAB sequences, the Zn(2+) binding motif was likely present in the primordial GatB/E, but became lost in certain lineages (e.g., S. aureus GatB). Two divalent metal binding sites, one permanent and the other transient, are present in the catalytic pocket of the A. aeolicus GatB. The two sites enable GatCAB to first phosphorylate the misacylated tRNA substrate and then amidate the activated intermediate to form the cognate products, Gln-tRNA(Gln) or Asn-tRNA(Asn).

PubMed: 19520089
DOI: 10.1016/j.jmb.2009.06.014

Experimental method

X-RAY DIFFRACTION (2.3 Å)