5B6A

Structure of Pyridoxal Kinasefrom Pseudomonas Aeruginosa

Summary for 5B6A

• Entry DOI: 10.2210/pdb5b6a/pdb
• Descriptor: Pyridoxal kinase PdxY, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: pseudomonas aeruginosa, pdxk, pyridoxal kinase, transferase
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
• Total number of polymer chains: 1
• Total formula weight: 31558.35

Authors

Kim, M.I.,Hong, M. (deposition date: 2016-05-25, release date: 2016-08-10, Last modification date: 2023-11-08)

Primary citation

Kim, M.I.,Hong, M.
Crystal structure and catalytic mechanism of pyridoxal kinase from Pseudomonas aeruginosa
Biochem.Biophys.Res.Commun., 478:300-306, 2016

PubMed Abstract: Pyridoxal kinase is a ubiquitous enzyme essential for pyridoxal 5'-phosphate (PLP) homeostasis since PLP is required for the catalytic activity of a variety of PLP-dependent enzymes involved in amino acid, lipid, and sugar metabolism as well as neurotransmitter biosynthesis. Previously, two catalytic mechanisms were proposed with regard to Pdx kinases, in which either the aspartate or the cysteine residue is involved as a catalytic residue. Because the Pdx kinase of Pseudomonas aeruginosa (PaPdxK) contains both residues, the catalytic mechanism of PaPdxK remains elusive. To elucidate the substrate-recognition and catalytic mechanisms of PaPdxK, the crystal structure of PaPdxK was determined at a 2.0 Å resolution. The PaPdxK structure possesses a channel that can accommodate substrates and a metallic cofactor. Our structure-based biochemical and mutational analyses in combination with modeling studies suggest that PaPdxK catalysis is mediated by an acid-base mechanism through the catalytic acid Asp225 and a helical dipole moment.

PubMed: 27425248
DOI: 10.1016/j.bbrc.2016.07.007

Experimental method

X-RAY DIFFRACTION (2 Å)