3A32

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix

Summary for 3A32

• Entry DOI: 10.2210/pdb3a32/pdb
• Related: 3A31
• Descriptor: Probable threonyl-tRNA synthetase 1, SULFATE ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: threonyl-trna synthetase, aeropyrum pernix k1, protein biosynthesis, aminoacyl-trna synthetase, atp-binding, ligase, metal-binding, nucleotide-binding
• Biological source: Aeropyrum pernix
• Cellular location: Cytoplasm (Potential): Q9YDW0
• Total number of polymer chains: 1
• Total formula weight: 53739.72

Authors

Shimizu, S.,Juan, E.C.M.,Miyashita, Y.,Sato, Y.,Hoque, M.M.,Suzuki, K.,Yogiashi, M.,Tsunoda, M.,Dock-Bregeon, A.-C.,Moras, D.,Sekiguchi, T.,Takenaka, A. (deposition date: 2009-06-07, release date: 2009-10-27, Last modification date: 2023-11-01)

Primary citation

Shimizu, S.,Juan, E.C.M.,Sato, Y.,Miyashita, Y.,Hoque, M.M.,Suzuki, K.,Sagara, T.,Tsunoda, M.,Sekiguchi, T.,Dock-Bregeon, A.-C.,Moras, D.,Takenaka, A.
Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain
J.Mol.Biol., 394:286-296, 2009

PubMed Abstract: In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA(Thr) from different tRNAs in order to generate Thr-tRNA(Thr). In general, an organism possesses one kind of gene corresponding to ThrRS. However, it has been recently found that some organisms have two different genes for ThrRS in the genome, suggesting that their proteins ThrRS-1 and ThrRS-2 function separately and complement each other in the threonylation of tRNA(Thr), one for catalysis and the other for trans-editing of misacylated Ser-tRNA(Thr). In order to clarify their three-dimensional structures, we performed X-ray analyses of two putatively assigned ThrRSs from Aeropyrum pernix (ApThrRS-1 and ApThrRS-2). These proteins were overexpressed in Escherichia coli, purified, and crystallized. The crystal structure of ApThrRS-1 has been successfully determined at 2.3 A resolution. ApThrRS-1 is a dimeric enzyme composed of two identical subunits, each containing two domains for the catalytic reaction and for anticodon binding. The essential editing domain is completely missing as expected. These structural features reveal that ThrRS-1 catalyzes only the aminoacylation of the cognate tRNA, suggesting the necessity of the second enzyme ThrRS-2 for trans-editing. Since the N-terminal sequence of ApThrRS-2 is similar to the sequence of the editing domain of ThrRS from Pyrococcus abyssi, ApThrRS-2 has been expected to catalyze deaminoacylation of a misacylated serine moiety at the CCA terminus.

PubMed: 19761773
DOI: 10.1016/j.jmb.2009.09.018

Experimental method

X-RAY DIFFRACTION (2.3 Å)