Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.

Kang, P.A.Oh, J.Lee, H.Witte, C.P.Rhee, S.

(2019) J Struct Biol 206: 110-118

  • DOI: https://doi.org/10.1016/j.jsb.2019.02.007
  • Primary Citation of Related Structures:  
    6ILR, 6ILS, 6ILT

  • 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 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.

  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
313Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g17160F20D23.14F20D23_14
Find proteins for A1A6H3 (Arabidopsis thaliana)
Explore A1A6H3 
Go to UniProtKB:  A1A6H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1A6H3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.46α = 90
b = 99.46β = 90
c = 165.74γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic OfPJ01325801
National Research Foundation (Korea)Korea, Republic Of2017R1A2B4002860

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary