3VQW

Crystal structure of the SeMet substituted catalytic domain of pyrrolysyl-tRNA synthetase

3VQW の概要

• エントリーDOI: 10.2210/pdb3vqw/pdb
• 関連するPDBエントリー: 2e3c 2zcd 2zce 2zin 2zio 3vqv 3vqx 3vqy
• 分子名称: Pyrrolysine--tRNA ligase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, aminoacyl-trna synthetase, pyrrolysyl-trna synthetase, amppnp, ligase
• 由来する生物種: Methanosarcina mazei
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34274.13

構造登録者

Yanagisawa, T.,Sumida, T.,Ishii, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2012-04-01, 公開日: 2013-01-02, 最終更新日: 2024-10-09)

主引用文献

Yanagisawa, T.,Sumida, T.,Ishii, R.,Yokoyama, S.
A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
Acta Crystallogr.,Sect.D, 69:5-15, 2013

PubMed Abstract: Structures of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) have been determined in a novel crystal form. The triclinic form crystals contained two PylRS dimers (four monomer molecules) in the asymmetric unit, in which the two subunits in one dimer each bind N(ℇ)-(tert-butyloxycarbonyl)-L-lysyladenylate (BocLys-AMP) and the two subunits in the other dimer each bind AMP. The BocLys-AMP molecules adopt a curved conformation and the C(α) position of BocLys-AMP protrudes from the active site. The β7-β8 hairpin structures in the four PylRS molecules represent distinct conformations of different states of the aminoacyl-tRNA synthesis reaction. Tyr384, at the tip of the β7-β8 hairpin, moves from the edge to the inside of the active-site pocket and adopts multiple conformations in each state. Furthermore, a new crystal structure of the BocLys-AMPPNP-bound form is also reported. The bound BocLys adopts an unusually bent conformation, which differs from the previously reported structure. It is suggested that the present BocLys-AMPPNP-bound, BocLys-AMP-bound and AMP-bound complexes represent the initial binding of an amino acid (or pre-aminoacyl-AMP synthesis), pre-aminoacyl-tRNA synthesis and post-aminoacyl-tRNA synthesis states, respectively. The conformational changes of Asn346 that accompany the aminoacyl-tRNA synthesis reaction have been captured by X-ray crystallographic analyses. The orientation of the Asn346 side chain, which hydrogen-bonds to the carbonyl group of the amino-acid substrate, shifts by a maximum of 85-90° around the C(β) atom.

PubMed: 23275158
DOI: 10.1107/S0907444912039881

実験手法

X-RAY DIFFRACTION (2.4 Å)