1G78

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION

Summary for 1G78

• Entry DOI: 10.2210/pdb1g78/pdb
• Related: 1G76 1G77
• Descriptor: PYRIDOXINE 5'-PHOSPHATE OXIDASE, PHOSPHATE ION, FLAVIN MONONUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: plp complex, fmn complex, pyridoxine 5'-phosphate, oxidoreductase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 26960.24

Authors

Safo, M.K.,Musayev, F.N.,di Salvo, M.L.,Schirch, V. (deposition date: 2000-11-09, release date: 2000-11-29, Last modification date: 2023-11-15)

Primary citation

Safo, M.K.,Musayev, F.N.,di Salvo, M.L.,Schirch, V.
X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution.
J.Mol.Biol., 310:817-826, 2001

PubMed Abstract: Escherichia coli pyridoxine 5'-phosphate oxidase catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate by the FMN oxidation of pyridoxine 5'-phosphate forming FMNH(2) and H(2)O(2). Recent studies have shown that in addition to the active site, pyridoxine 5'-phosphate oxidase contains a non-catalytic site that binds pyridoxal 5'-phosphate tightly. The crystal structure of pyridoxine 5'-phosphate oxidase from E. coli with one or two molecules of pyridoxal 5'-phosphate bound to each monomer has been determined to 2.0 A resolution. One of the pyridoxal 5'-phosphate molecules is clearly bound at the active site with the aldehyde at C4' of pyridoxal 5'-phosphate near N5 of the bound FMN. A protein conformational change has occurred that partially closes the active site. The orientation of the bound pyridoxal 5'-phosphate suggests that the enzyme catalyzes a hydride ion transfer between C4' of pyridoxal 5'-phosphate and N5 of FMN. When the crystals are soaked with excess pyridoxal 5'-phosphate an additional molecule of this cofactor is also bound about 11 A from the active site. A possible tunnel exists between the two sites so that pyridoxal 5'-phosphate formed at the active site may transfer to the non-catalytic site without passing though the solvent.

PubMed: 11453690
DOI: 10.1006/jmbi.2001.4734

Experimental method

X-RAY DIFFRACTION (2.2 Å)