6ILT

Structure of Arabidopsis thaliana Ribokinase complexed with ATP and Magnesium ion

Summary for 6ILT

• Entry DOI: 10.2210/pdb6ilt/pdb
• Descriptor: Ribokinase, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: ribose, ribokinase, atrbsk, pfkb family, phosphotransferase, transferase
• Biological source: Arabidopsis thaliana (Mouse-ear cress)
• Total number of polymer chains: 2
• Total formula weight: 67015.37

Authors

Kang, P.,Oh, J.,Rhee, S. (deposition date: 2018-10-19, release date: 2019-03-13, Last modification date: 2023-11-22)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.2 Å)