An Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase

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dc.contributor.authorRamirez-Sarmiento, Cesar A.
dc.contributor.authorEngelberger, Felipe
dc.contributor.authorGuixe, Victoria
dc.date.accessioned2025-01-23T19:50:16Z
dc.date.available2025-01-23T19:50:16Z
dc.date.issued2020
dc.description.abstractThe ribokinase superfamily catalyzes the phosphorylation of a vast diversity of substrates, and its members are characterized by the conservation of a common structural fold along with highly conserved sequence motifs responsible for phosphoryl transfer (GXGD) and stabilization of the metal-nucleotide complex (NXXE). Recently, a third motif (HXE) exclusive from ADP-dependent enzymes was identified, with its glutamic acid participating in water-mediated interactions with the metal-nucleotide complex and in stabilization of the ternary complex during catalysis. In this work, we bioinformatically determine that the aspartic acid of another motif (DPV), exclusively found in hydroxyethyl thiazole (THZK), hydroxymethyl pyrimidine (HMPK) and pyridoxal kinases (PLK), is structurally equivalent to the acidic residue in the HXE motif. Moreover, this residue is highly conserved among all ribokinase superfamily members. To determine whether the functional role of the DPV motif is similar to the HXE motif, we employed molecular dynamics simulations using crystal structures of phosphoryl donor substrate-complexed THZK and PLK, showing that its aspartic acid participated in water-mediated or direct interactions with the divalent metal of the metal-nucleotide complex. Lastly, enzyme kinetic assays on human PLK, an enzyme that utilizes zinc, showed that site-directed mutagenesis of the aspartic acid from the DPV motif abolishes the inhibition of this enzyme by increasing free zinc concentrations. Altogether, our results highlight that the DPV and HXE motifs are evolutionary markers of the functional and structural divergence of the ribokinase superfamily and evidence the role of the DPV motif in the interaction with both free and nucleotide-complexed divalent metals in the binding site of these enzymes.
dc.description.funderFondo Nacional de Desarrollo Cientifico y Tecnologico (Fondecyt)
dc.fuente.origenWOS
dc.identifier.doi10.3390/catal10050555
dc.identifier.eissn2073-4344
dc.identifier.urihttps://doi.org/10.3390/catal10050555
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/100545
dc.identifier.wosidWOS:000546007000128
dc.issue.numero5
dc.language.isoen
dc.revistaCatalysts
dc.rightsacceso restringido
dc.subjectpyridoxal kinase
dc.subjectenzyme activity
dc.subjectzinc regulation
dc.subjectmetal-assisted catalysis
dc.subjectevolution
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleAn Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase
dc.typeartículo
dc.volumen10
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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