Details
| Original language | English |
|---|---|
| Pages (from-to) | 110-118 |
| Number of pages | 9 |
| Journal | Journal of structural biology |
| Volume | 206 |
| Issue number | 1 |
| Early online date | 26 Feb 2019 |
| Publication status | Published - 1 Apr 2019 |
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 2+ . 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 2+ , ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg 2+ 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.
Keywords
- Arabidopsis, Enzyme catalysis, Nucleoside metabolism, Protein structure, Ribokinase
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Structural Biology
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In: Journal of structural biology, Vol. 206, No. 1, 01.04.2019, p. 110-118.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana
AU - Kang, Pyeoung-Ann
AU - Oh, Juntaek
AU - Lee, Haehee
AU - Witte, Claus-Peter
AU - Rhee, Sangkee
N1 - Funding Information: This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ01325801 ), Rural Development Administration of Korea , and also by the National Research Foundation of Korea Grant ( 2017R1A2B4002860 ) from MSIP, Korea.
PY - 2019/4/1
Y1 - 2019/4/1
N2 - 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 2+ . 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 2+ , ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg 2+ 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.
AB - 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 2+ . 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 2+ , ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg 2+ 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.
KW - Arabidopsis
KW - Enzyme catalysis
KW - Nucleoside metabolism
KW - Protein structure
KW - Ribokinase
UR - http://www.scopus.com/inward/record.url?scp=85062422390&partnerID=8YFLogxK
U2 - 10.1016/j.jsb.2019.02.007
DO - 10.1016/j.jsb.2019.02.007
M3 - Article
VL - 206
SP - 110
EP - 118
JO - Journal of structural biology
JF - Journal of structural biology
SN - 1047-8477
IS - 1
ER -