6ILS

Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP

6ILS の概要

• エントリーDOI: 10.2210/pdb6ils/pdb
• 分子名称: Ribokinase, ADENOSINE-5'-TRIPHOSPHATE, SODIUM ION, ... (5 entities in total)
• 機能のキーワード: ribose, ribokinase, atrbsk, pfkb family, phosphotransferase, transferase
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 67068.28

構造登録者

Kang, P.,Oh, J.,Rhee, S. (登録日: 2018-10-19, 公開日: 2019-03-13, 最終更新日: 2023-11-22)

主引用文献

Kang, P.A.,Oh, J.,Lee, H.,Witte, C.P.,Rhee, S.
Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.
J. Struct. Biol., 206:110-118, 2019

PubMed Abstract: Nitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides. In this study, we report the crystal structure of RBSK from Arapidopsis thaliana (AtRBSK) in three different ligation states: an unliganded state, a ternary complex with ribose and ATP, and a binary complex with ATP in the presence of Mg. In the monomeric conformation, AtRBSK is highly homologous to bacterial RBSKs, including the binding sites for a monovalent cation, ribose, and ATP. Its dimeric conformation, however, does not exhibit the noticeable ligand-induced changes that were observed in bacterial orthologs. Only in the presence of Mg, ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg in AtRBSK activity. The structural data combined with activity analyses of mutants allowed assignment of functional roles for the active site residues. Overall, this study provides the first structural characterization of plant RBSK, and experimentally validates a previous hypothetical model concerning the general reaction mechanism of RBSK.

PubMed: 30822455
DOI: 10.1016/j.jsb.2019.02.007

実験手法

X-RAY DIFFRACTION (1.8 Å)