8TF1

Crystal Structure of Pyridoxal Reductase (PDXI)in complex with NADPH and Pyridoxal

Summary for 8TF1

• Entry DOI: 10.2210/pdb8tf1/pdb
• Descriptor: Pyridoxine 4-dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol, ... (5 entities in total)
• Functional Keywords: pdxi, aldo-keto reductases superfamily, vitamin b6, nadph, pyridoxal, oxidoreductase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 33844.15

Authors

Donkor, A.K.,Safo, M.K.,Musayev, F.N. (deposition date: 2023-07-07, release date: 2024-12-18, Last modification date: 2025-07-02)

Primary citation

Tramonti, A.,Donkor, A.K.,Parroni, A.,Musayev, F.N.,Barile, A.,Ghatge, M.S.,Graziani, C.,Alkhairi, M.,AlAwadh, M.,di Salvo, M.L.,Safo, M.K.,Contestabile, R.
Functional and structural properties of pyridoxal reductase (PdxI) from Escherichia coli: a pivotal enzyme in the vitamin B6 salvage pathway.
Febs J., 290:5628-5651, 2023

PubMed Abstract: Pyridoxine 4-dehydrogenase (PdxI), a NADPH-dependent pyridoxal reductase, is one of the key players in the Escherichia coli pyridoxal 5'-phosphate (PLP) salvage pathway. This enzyme, which catalyses the reduction of pyridoxal into pyridoxine, causes pyridoxal to be converted into PLP via the formation of pyridoxine and pyridoxine phosphate. The structural and functional properties of PdxI were hitherto unknown, preventing a rational explanation of how and why this longer, detoured pathway occurs, given that, in E. coli, two pyridoxal kinases (PdxK and PdxY) exist that could convert pyridoxal directly into PLP. Here, we report a detailed characterisation of E. coli PdxI that explains this behaviour. The enzyme efficiently catalyses the reversible transformation of pyridoxal into pyridoxine, although the reduction direction is thermodynamically strongly favoured, following a compulsory-order ternary-complex mechanism. In vitro, the enzyme is also able to catalyse PLP reduction and use NADH as an electron donor, although with lower efficiency. As with all members of the aldo-keto reductase (AKR) superfamily, the enzyme has a TIM barrel fold; however, it shows some specific features, the most important of which is the presence of an Arg residue that replaces the catalytic tetrad His residue that is present in all AKRs and appears to be involved in substrate specificity. The above results, in conjunction with kinetic and static measurements of vitamins B in cell extracts of E. coli wild-type and knockout strains, shed light on the role of PdxI and both kinases in determining the pathway followed by pyridoxal in its conversion to PLP, which has a precise regulatory function.

PubMed: 37734924
DOI: 10.1111/febs.16962

Experimental method

X-RAY DIFFRACTION (2 Å)