5DK4

Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP

5DK4 の概要

• エントリーDOI: 10.2210/pdb5dk4/pdb
• 分子名称: Tryptophan--tRNA ligase, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (6 entities in total)
• 機能のキーワード: aars, inhibitor, ligase-ligase inhibitor complex, ligase/ligase inhibitor
• 由来する生物種: Geobacillus stearothermophilus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38632.54

構造登録者

Williams, T.,Yin, W.Y.,Carter Jr., C.W. (登録日: 2015-09-02, 公開日: 2015-11-18, 最終更新日: 2024-10-23)

主引用文献

Williams, T.L.,Yin, Y.W.,Carter, C.W.
Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based.
J.Biol.Chem., 291:255-265, 2016

PubMed Abstract: Indolmycin is a natural tryptophan analog that competes with tryptophan for binding to tryptophanyl-tRNA synthetase (TrpRS) enzymes. Bacterial and eukaryotic cytosolic TrpRSs have comparable affinities for tryptophan (Km ∼ 2 μm), and yet only bacterial TrpRSs are inhibited by indolmycin. Despite the similarity between these ligands, Bacillus stearothermophilus (Bs)TrpRS preferentially binds indolmycin ∼1500-fold more tightly than its tryptophan substrate. Kinetic characterization and crystallographic analysis of BsTrpRS allowed us to probe novel aspects of indolmycin inhibitory action. Previous work had revealed that long range coupling to residues within an allosteric region called the D1 switch of BsTrpRS positions the Mg(2+) ion in a manner that allows it to assist in transition state stabilization. The Mg(2+) ion in the inhibited complex forms significantly closer contacts with non-bridging oxygen atoms from each phosphate group of ATP and three water molecules than occur in the (presumably catalytically competent) pre-transition state (preTS) crystal structures. We propose that this altered coordination stabilizes a ground state Mg(2+)·ATP configuration, accounting for the high affinity inhibition of BsTrpRS by indolmycin. Conversely, both the ATP configuration and Mg(2+) coordination in the human cytosolic (Hc)TrpRS preTS structure differ greatly from the BsTrpRS preTS structure. The effect of these differences is that catalysis occurs via a different transition state stabilization mechanism in HcTrpRS with a yet-to-be determined role for Mg(2+). Modeling indolmycin into the tryptophan binding site points to steric hindrance and an inability to retain the interactions used for tryptophan substrate recognition as causes for the 1000-fold weaker indolmycin affinity to HcTrpRS.

PubMed: 26555258
DOI: 10.1074/jbc.M115.690321

実験手法

X-RAY DIFFRACTION (1.9 Å)