2YXU

Human Pyridoxal Kinase

Summary for 2YXU

• Entry DOI: 10.2210/pdb2yxu/pdb
• Related: 1LHP 2YXT
• Descriptor: Pyridoxal kinase, MAGNESIUM ION, SODIUM ION, ... (7 entities in total)
• Functional Keywords: beta sheet with alpha helix, atp complex, metal ion, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: O00764
• Total number of polymer chains: 2
• Total formula weight: 73288.43

Authors

Safo, M.K.,Musayev, F.N.,Ko, T.P.,Schirch, V. (deposition date: 2007-04-27, release date: 2008-03-11, Last modification date: 2023-10-25)

Primary citation

Musayev, F.N.,di Salvo, M.L.,Ko, T.P.,Gandhi, A.K.,Goswami, A.,Schirch, V.,Safo, M.K.
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Protein Sci., 16:2184-2194, 2007

PubMed Abstract: Pyridoxal kinase catalyzes the transfer of a phosphate group from ATP to the 5' alcohol of pyridoxine, pyridoxamine, and pyridoxal. In this work, kinetic studies were conducted to examine monovalent cation dependence of human pyridoxal kinase kinetic parameters. The results show that hPLK affinity for ATP and PL is increased manyfold in the presence of K(+) when compared to Na(+); however, the maximal activity of the Na(+) form of the enzyme is more than double the activity in the presence of K(+). Other monovalent cations, Li(+), Cs(+), and Rb(+) do not show significant activity. We have determined the crystal structure of hPLK in the unliganded form, and in complex with MgATP to 2.0 and 2.2 A resolution, respectively. Overall, the two structures show similar open conformation, and likely represent the catalytically idle state. The crystal structure of the MgATP complex also reveals Mg(2+) and Na(+) acting in tandem to anchor the ATP at the active site. Interestingly, the active site of hPLK acts as a sink to bind several molecules of MPD. The features of monovalent and divalent metal cation binding, active site structure, and vitamin B6 specificity are discussed in terms of the kinetic and structural studies, and are compared with those of the sheep and Escherichia coli enzymes.

PubMed: 17766369
DOI: 10.1110/ps.073022107

Experimental method

X-RAY DIFFRACTION (2.2 Å)