Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation

  • Rakhi Paul
  • Madhumita Dandopath Patra
  • Udayaditya SenEmail author
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 842)


Ribokinase (RK; EC catalyzes the transfer of γ-phosphate from adenosine tri-phosphate (ATP) to O5′ of d-ribose to form d-ribose-5-phosphate, a key step that enables d-ribose to enter into the metabolic pathways for further use. The phosphorylation reaction of ribose by RK is catalyzed by divalent cations whereas monovalent cations activate RK and allosterically regulate the reaction. In order to gain further insights into the catalytic functions of RK, crystal structures of Vibrio cholerae ribokinase (Vc-RK) have been solved in apo form (3.4 Å), sugar + ADP bound form (1.75 Å) and sugar + ADP + Cs+ (2.37 Å) bound form and compared with E. coli RK and Sa239 RK. Vc-RK, like E. coli RK and Sa239 RK, exists as a dimer and each monomer has two domains, a large catalytic α/β domain consisting of a central nine stranded twisted β-sheet which is flanked on both faces by five α-helices and a four stranded β-sheet region protruding from the α/β domain. The structure of Vc-RK in sugar + ADP bound form when compared with Cs+ bound E. coli RK structure is seen to be activated by a Na+ ion. The location of the Na+ ion is confirmed by the sugar + ADP + Cs+ bound Vc-RK structure where Cs+ occupies the same position as Na+. Comparisons between the apo and ligand bound Vc-RK structures have allowed us to identify the conformational changes associated with the activation in the presence of Na+, sugar induced structural changes and mechanism of phosphorylation reaction of Vc-RK.



The laboratory of US is supported by the MSACR project, DAE, Government of India and SINP. This work is supported by the Department of Biotechnology (DBT), Government of India (The BM14 beamline project for synchrotron data collection at the ESRF, Grenoble). M.D.P. thanks the DBT for a DBT-RA fellowship.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Rakhi Paul
    • 1
  • Madhumita Dandopath Patra
    • 1
  • Udayaditya Sen
    • 1
    Email author
  1. 1.Crystallography and Molecular Biology DivisionSaha Institute of Nuclear PhysicsKolkataIndia

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