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Conformational changes in the reaction of pyridoxal kinase.

Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC
J Biol Chem 279 17459-65 (2004)
Related entries: 1lhp, 1lhr, 1rft, 1rfv

Cited: 20 times
EuropePMC logo PMID: 14722069

Abstract

To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK),1 we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparisons of these structures have revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaced ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A apart, indicating that the position of ATP is not favorable to spontaneous transfer of its phosphate group. However, the structure of PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.

Articles - 1rfu mentioned but not cited (1)

  1. Purification, crystallization and preliminary X-ray diffraction analysis of pyridoxal kinase from Plasmodium falciparum (PfPdxK). Kronenberger T, Lunev S, Wrenger C, Groves MR. Acta Crystallogr F Struct Biol Commun 70 1550-1555 (2014)


Reviews citing this publication (3)

  1. Mitochondrial function and toxicity: role of B vitamins on the one-carbon transfer pathways. Depeint F, Bruce WR, Shangari N, Mehta R, O'Brien PJ. Chem Biol Interact 163 113-132 (2006)
  2. Vitamin B₆ and Its Role in Cell Metabolism and Physiology. Parra M, Stahl S, Hellmann H. Cells 7 E84 (2018)
  3. Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate. Meloni M, Gurrieri L, Fermani S, Velie L, Sparla F, Crozet P, Henri J, Zaffagnini M. Front Plant Sci 14 1130430 (2023)

Articles citing this publication (16)

  1. Convergent evolution of enzyme active sites is not a rare phenomenon. Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. J Mol Biol 372 817-845 (2007)
  2. A comprehensive survey of small-molecule binding pockets in proteins. Gao M, Skolnick J. PLoS Comput Biol 9 e1003302 (2013)
  3. Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle. Yu A, Xie Y, Pan X, Zhang H, Cao P, Su X, Chang W, Li M. Plant Cell 32 1556-1573 (2020)
  4. 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)
  5. 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)
  6. Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK. Protein Sci 16 2184-2194 (2007)
  7. 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)
  8. Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition. Gandhi AK, Desai JV, Ghatge MS, di Salvo ML, Di Biase S, Danso-Danquah R, Musayev FN, Contestabile R, Schirch V, Safo MK. PLoS One 7 e40954 (2012)
  9. 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)
  10. Crystal structure of human pyridoxal kinase. Cao P, Gong Y, Tang L, Leung YC, Jiang T. J Struct Biol 154 327-332 (2006)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. Biochemical Characterization and Structural Insight into Interaction and Conformation Mechanisms of Serratia marcescens Lysine Decarboxylase (SmcadA). Osire T, Qiao Z, Yang T, Xu M, Zhang X, Rao Z. Molecules 26 697 (2021)
  16. New Insights Into Pyridoxal Kinase Inhibitors and Their Antileukemic Effects. Banerjee P, Singh T, Qamar I. Cureus 15 e48176 (2023)


Related citations provided by authors (2)

  1. 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)
  2. 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 1479-81 (2002)

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