2YXT image
Deposition Date 2007-04-27
Release Date 2008-03-11
Last Version Date 2023-10-25
Entry Detail
PDB ID:
2YXT
Keywords:
Title:
Human Pyridoxal Kinase
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Pyridoxal kinase
Gene (Uniprot):PDXK
Chain IDs:A, B
Chain Length:312
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Protein Sci. 16 2184 2194 (2007)
PMID: 17766369 DOI: 10.1110/ps.073022107

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures