2E3C

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase

2E3C の概要

• エントリーDOI: 10.2210/pdb2e3c/pdb
• 関連するPDBエントリー: 2DXG 2DXH 2DZ8
• 分子名称: Pyrrolysyl-tRNA synthetase (2 entities in total)
• 機能のキーワード: aminoacyl-trna synthetase, trna, pyrrolysine, translation, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase
• 由来する生物種: Methanosarcina mazei
• 細胞内の位置: Cytoplasm (By similarity): Q8PWY1
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 33344.16

構造登録者

Yanagisawa, T.,Ishii, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2006-11-22, 公開日: 2007-12-11, 最終更新日: 2023-10-25)

主引用文献

Yanagisawa, T.,Ishii, R.,Fukunaga, R.,Kobayashi, T.,Sakamoto, K.,Yokoyama, S.
Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase
J.Mol.Biol., 378:634-652, 2008

PubMed Abstract: Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta 7-beta 8 hairpin exhibits multiple conformational states, the open, intermediate (beta 7-open/beta 8-open and beta 7-closed/beta 8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta 7-beta 8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta 7-beta 8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.

PubMed: 18387634
DOI: 10.1016/j.jmb.2008.02.045

実験手法

X-RAY DIFFRACTION (2.65 Å)