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Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate

Deka, Geeta and Kalyani, Josyula N and Jahangir, Fathima Benazir and Sabharwal, Pallavi and Savithri, Handanahal S and Murthy, Mathur R N (2019) Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate. In: FEBS JOURNAL, 286 (18). pp. 3684-3700.

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Official URL: https://dx.doi.org/10.1111/febs.14933

Abstract

A large number of enzymes depend on the ubiquitous cofactor pyridoxal 5 ` phosphate (PLP) for their activity. Pyridoxal kinase (PLK) is the key enzyme involved in the synthesis of PLP from the three forms of vitamin B-6 via the salvage pathway. In the present work, we determined the unliganded structure of StPLK in a monoclinic form and its ternary complex with bound pyridoxal (PL), ADP and Mg2+ in two different tetragonal crystal forms (Form I and Form II). We found that, in the ternary complex structure of StPLK, the active site Lys233 forms a Schiff base linkage with the substrate (PL). Although formation of a Schiff base with the active site Lys229 was demonstrated in the Escherichia coli enzyme based on biochemical studies, the ternary complex of StPLK represents the first crystal structure where the Schiff bond formation has been observed. We also identified an additional site for PLP binding away from the active site in one of the ternary complexes (crystal Form I), suggesting a probable route for the product release. This is the first ternary complex structure where the modeled gamma-phosphate of ATP is close enough to PL for the phosphorylation of the substrate. StPLK prefers PL over pyridoxamine as its substrate and follows a sequential mechanism of catalysis. Surface plasmon resonance studies suggest that StPLK interacts with apo-PLP-dependent enzymes with mu m affinity supporting the earlier proposed direct transfer mechanism of PLP from PLK to PLP-dependent enzymes.

Item Type: Journal Article
Additional Information: copyright for this article belongs to WILEY
Keywords: pyridoxal; pyridoxal 5MODIFIER LETTER PRIME phosphate; pyridoxal kinase; Schiff base; X-ray crystallography
Department/Centre: Division of Biological Sciences > Biochemistry
Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 21 Oct 2019 09:43
Last Modified: 21 Oct 2019 09:43
URI: http://eprints.iisc.ac.in/id/eprint/63729

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