2DDW

Crystal Structure of Pyridoxal Kinase from the Escherichia coli PdxK gene complexed with pyridoxal at 3.2 A resolution

Summary for 2DDW

• Entry DOI: 10.2210/pdb2ddw/pdb
• Related: 2DDM 2DDO
• Descriptor: Pyridoxine kinase, 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE (3 entities in total)
• Functional Keywords: pyridoxal kinase, ribokinase, pyridoxal 5'-phosphate, vitamin b6, phosphorylation, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 62086.91

Authors

Safo, M.K.,Musayev, F.N.,di Salvo, M.L.,Hunt, S.,Claude, J.B.,Schirch, V. (deposition date: 2006-02-03, release date: 2006-08-15, Last modification date: 2023-10-25)

Primary citation

Safo, M.K.,Musayev, F.N.,di Salvo, M.L.,Hunt, S.,Claude, J.B.,Schirch, V.
Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.
J.Bacteriol., 188:4542-4552, 2006

PubMed Abstract: The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.

PubMed: 16740960
DOI: 10.1128/JB.00122-06

Experimental method

X-RAY DIFFRACTION (3.2 Å)