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Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.

Li MH, Kwok F, Chang WR, Lau CK, Zhang JP, Lo SC, Jiang T, Liang DC
J Biol Chem 277 46385-90 (2002)
Cited: 42 times
EuropePMC logo PMID: 12235162

Abstract

The three-dimensional structures of brain pyridoxal kinase and its complex with the nucleotide ATP have been elucidated in the dimeric form at 2.1 and 2.6 A, respectively. Results have shown that pyridoxal kinase, as an enzyme obeying random sequential kinetics in catalysis, does not possess a lid shape structure common to all kinases in the ribokinase superfamily. This finding has been shown to be in line with the condition that pyridoxal kinase binds substrates with variable sizes of chemical groups at position 4 of vitamin B(6) and its derivatives. In addition, the enzyme contains a 12-residue peptide loop in the active site for the prevention of premature hydrolysis of ATP. Conserved amino acid residues Asp(118) and Tyr(127) in the peptide loop could be moved to a position covering the nucleotide after its binding so that its chance to hydrolyze in the aqueous environment of the active site was reduced. With respect to the evolutionary trend of kinase enzymes, the existence of this loop in pyridoxal kinase could be classified as an independent category in the ribokinase superfamily according to the structural feature found and mechanism followed in catalysis.

Articles - 1lhr mentioned but not cited (3)

  1. Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases. Safo MK, Musayev FN, di Salvo ML, Hunt S, Claude JB, Schirch V. J Bacteriol 188 4542-4552 (2006)
  2. Crystal structure of the PdxY Protein from Escherichia coli. Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V. J Bacteriol 186 8074-8082 (2004)
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  1. Role of Na+ and K+ in enzyme function. Page MJ, Di Cera E. Physiol Rev 86 1049-1092 (2006)
  2. Vitamin B6: a long known compound of surprising complexity. Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Molecules 14 329-351 (2009)
  3. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. Gohara DW, Di Cera E. J Biol Chem 291 20840-20848 (2016)
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  5. The ADP-dependent sugar kinase family: kinetic and evolutionary aspects. Guixé V, Merino F. IUBMB Life 61 753-761 (2009)

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  3. Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases. Giardina G, Montioli R, Gianni S, Cellini B, Paiardini A, Voltattorni CB, Cutruzzolà F. Proc Natl Acad Sci U S A 108 20514-20519 (2011)
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  5. Pyridoxal 5'-phosphate is a slow tight binding inhibitor of E. coli pyridoxal kinase. Ghatge MS, Contestabile R, di Salvo ML, Desai JV, Gandhi AK, Camara CM, Florio R, González IN, Parroni A, Schirch V, Safo MK. PLoS One 7 e41680 (2012)
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  7. Vitamin B1 de novo synthesis in the human malaria parasite Plasmodium falciparum depends on external provision of 4-amino-5-hydroxymethyl-2-methylpyrimidine. Wrenger C, Eschbach ML, Müller IB, Laun NP, Begley TP, Walter RD. Biol Chem 387 41-51 (2006)
  8. Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. di Salvo ML, Hunt S, Schirch V. Protein Expr Purif 36 300-306 (2004)
  9. Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. McArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA. J Bacteriol 187 5292-5300 (2005)
  10. Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate. Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH. J Mol Biol 340 477-489 (2004)
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  13. The phosphofructokinase-B (MJ0406) from Methanocaldococcus jannaschii represents a nucleoside kinase with a broad substrate specificity. Hansen T, Arnfors L, Ladenstein R, Schönheit P. Extremophiles 11 105-114 (2007)
  14. A system of protein target sequences for anti-RNA-viral chemotherapy by a vitamin B6-derived zinc-chelating trioxa-adamantane-triol. Kesel AJ. Bioorg Med Chem 11 4599-4613 (2003)
  15. Chemical, genetic and structural assessment of pyridoxal kinase as a drug target in the African trypanosome. Jones DC, Alphey MS, Wyllie S, Fairlamb AH. Mol Microbiol 86 51-64 (2012)
  16. Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Gandhi AK, Ghatge MS, Musayev FN, Sease A, Aboagye SO, di Salvo ML, Schirch V, Safo MK. Biochem Biophys Res Commun 381 12-15 (2009)
  17. Specificity evolution of the ADP-dependent sugar kinase family: in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii. Merino F, Guixé V. FEBS J 275 4033-4044 (2008)
  18. The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution. Newman JA, Das SK, Sedelnikova SE, Rice DW. J Mol Biol 363 520-530 (2006)
  19. Crystal structure of human pyridoxal kinase. Cao P, Gong Y, Tang L, Leung YC, Jiang T. J Struct Biol 154 327-332 (2006)
  20. Reversible unfolding of dimeric phosphofructokinase-2 from Escherichia coli reveals a dominant role of inter-subunit contacts for stability. Baez M, Babul J. FEBS Lett 583 2054-2060 (2009)
  21. Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission. Kasaragod VB, Pacios-Michelena A, Schaefer N, Zheng F, Bader N, Alzheimer C, Villmann C, Schindelin H. Proc Natl Acad Sci U S A 117 33235-33245 (2020)
  22. The expression of four pyridoxal kinase (PDXK) human variants in Drosophila impacts on genome integrity. Mascolo E, Barile A, Mecarelli LS, Amoroso N, Merigliano C, Massimi A, Saggio I, Hansen T, Tramonti A, Di Salvo ML, Barbetti F, Contestabile R, Vernì F. Sci Rep 9 14188 (2019)
  23. Cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from Bacillus subtilis. Newman JA, Das SK, Sedelnikova SE, Rice DW. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 1006-1009 (2006)
  24. Inhibition of human pyridoxal kinase by 2-acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI). Elsinghorst PW, di Salvo ML, Parroni A, Contestabile R. J Enzyme Inhib Med Chem 30 336-340 (2015)
  25. Key Factors for A One-Pot Enzyme Cascade Synthesis of High Molecular Weight Hyaluronic Acid. Gottschalk J, Zaun H, Eisele A, Kuballa J, Elling L. Int J Mol Sci 20 E5664 (2019)
  26. Catalytic and regulatory roles of species involved in metal-nucleotide equilibriums in human pyridoxal kinase. Navarro F, Ramírez-Sarmiento CA, Guixé V. Biometals 26 805-812 (2013)
  27. Dissecting the functional roles of the conserved NXXE and HXE motifs of the ADP-dependent glucokinase from Thermococcus litoralis. Abarca-Lagunas MJ, Rivas-Pardo JA, Ramírez-Sarmiento CA, Guixé V. FEBS Lett 589 3271-3276 (2015)
  28. Insights Into Histoplasma capsulatum Behavior on Zinc Deprivation. Assunção LDP, Moraes D, Soares LW, Silva-Bailão MG, de Siqueira JG, Baeza LC, Báo SN, Soares CMA, Bailão AM. Front Cell Infect Microbiol 10 573097 (2020)
  29. Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP-dependent vitamin kinase family members. Gonzalez-Ordenes F, Bravo-Moraga F, Gonzalez E, Hernandez-Cabello L, Alzate-Morales J, Guixé V, Castro-Fernandez V. Protein Sci 30 842-854 (2021)
  30. Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions. Dyguda-Kazimierowicz E, Sokalski WA, Leszczyński J. J Mol Model 13 839-849 (2007)
  31. Expression analysis of a novel pyridoxal kinase messenger RNA splice variant, PKL, in oil rape suffering abiotic stress and phytohormones. Yu S, Luo L. Acta Biochim Biophys Sin (Shanghai) 40 1005-1014 (2008)
  32. New Insights Into Pyridoxal Kinase Inhibitors and Their Antileukemic Effects. Banerjee P, Singh T, Qamar I. Cureus 15 e48176 (2023)
  33. Proteomic characterization of spontaneously regrowing spinal cord following injury in the teleost fish Apteronotus leptorhynchus, a regeneration-competent vertebrate. Sîrbulescu RF, Ilieş I, Amelung L, Zupanc GKH. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 208 671-706 (2022)
  34. Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK). Deka G, Kalyani JN, Benazir JF, Savithri HS, Murthy MR. Acta Crystallogr F Struct Biol Commun 70 526-529 (2014)


Related citations provided by authors (1)

  1. Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain. Li MH, Kwok F, An XM, Chang WR, Lau CK, Zhang JP, Liu SQ, Leung YC, Jiang T, Liang DC Acta Crystallogr. D Biol. Crystallogr. 58 1479-1481 (2002)

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