Article /  Structural Insights into the β-Clasp and Dimerization Interface of Human RibokinaseArticle /  Structural Insights into the β-Clasp and Dimerization Interface of Human RibokinaseArticle /  Structural Insights into the β-Clasp and Dimerization Interface of Human RibokinaseArticle /  Structural Insights into the β-Clasp and Dimerization Interface of Human Ribokinase
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  • RESEARCH CENTERS
  • CORE FACILITIES
    • Advanced Microscopy
    • Cell Culture
    • Molecular Cell Biology
    • Proteomics
    • Drug Discovery
    • Bioinformatics
    • Biomaterials
    • Electrophysiology and Behavior
    • Cognitive Neuroscience
  • PEOPLE
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    • Group Leader
    • Transition Scientist
    • Early Career Researchers
    • Students
  • EVENTS
    • Event Calendar
    • Critical Mind
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Article / Structural Insights into the β-Clasp and Dimerization Interface of Human Ribokinase

Structural Insights into the β-Clasp and Dimerization Interface of Human Ribokinase

Juliana C. Ferreira, Adrian J. Villanueva, Samar Fadl, Zhandos Shegenov, Zeynep Nur Cinviz, Ozge Sensoy, Wael M. Rabeh

Ribokinase (RK), a member of the phosphofructokinase B (PfkB) family, catalyzes the ATP-dependent phosphorylation of d-ribose to ribose-5-phosphate, a step essential for nucleotide biosynthesis and pentose phosphate pathway flux. Because these pathways support redox balance, energy metabolism, and cell proliferation, RK is relevant to cancer and ischemic injury. A conserved feature of PfkB enzymes is the β-clasp dimerization motif, an interlocking β-strand interface between protomers. However, its quantitative contribution to human RK stability and catalysis remains unclear. Here, we define the structural and functional role of the RK β-clasp using structure-guided mutagenesis and integrated functional analyses. The β-clasp contains two interaction layers: (1) a β3a–β7 backbone hydrogen-bond networkthat forms the core dimer scaffold and (2) a surrounding network of polar and hydrophobic interactions that reinforce the interface. Alanine substitutions disrupting individual polar interactions were largely tolerated, preserving dimerization, near-wild-type activity, and thermal stability. However, disruption of the V122/V124-centered hydrophobic core reduced catalytic turnover with minimal effects on substrate affinity, indicating that the β-clasp primarily supports catalytic competence rather than substrate recognition. Progressive β3a deletions destabilized the dimer in a graded manner, yielding inactive, predominantly monomeric variants with noncooperative biphasic thermal unfolding transitions, although far-UV circular dichroism confirmed retention of the α/β fold. Molecular dynamics simulations showed that disruptive variants increased β-clasp flexibility, weakened the Asp27-centered ribose-binding network, and reduced ribose retention. Together, these findings identify the β-clasp as a conformational hub coupling dimerization to lid positioning and productive phosphoryl transfer, establishing it as a potential allosteric target for regulation.

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