Pyridoxal phosphate binding site

Kabil O, Toaka S, LoBrutto R, Shoemaker R, and Banerjee R (2001) Pyridoxal phosphate binding sites are similar in human heme-dependent and yeast heme-independent cystathionine beta-synthases. Evidence from P NMR and pulsed EPR spectroscopy that heme and PLP cofactors are not proximal in the human enzyme. Journal of Biological Chemistry 276,19350-5. 

Parsons TF, Preiss J. Biosynthesis of bacterial glycogen. Incorporation of pyridoxal phosphate into the allosteric activator site and an ADP-glucose-protected pyridoxal phosphate binding site of Escherichia coli B ADP-glucose synthase. J. Biol. Chem. 1978 253 6197-6202. 

Anai, M., Lai, C.Y., and Horecker, B.L. (1973) The pyridoxal phosphate-binding site of rabbit muscle aldolase. Arch. Bio-chem. Biophys. 156, 712-719. 

The location of the two pyridoxal phosphate modification sites is of obvious interest, since they provide a marker for the reductase binding site. In the preliminary report 218), three pyridoxal phosphate-containing peptides were found residues 1-10, 68-74, and 83-94. Candidates for modification therefore include lysines 5, 7, 8, 86, 87, and 88 at the top of the molecule, and 72 and 73 on the left side. The further narrowing down of these groups will be awaited with great interest. 

Applebaum, D., Sabo, D.L., Fischer, E.H., and Morris, D.R. (1975) Biodegradative ornithine decarboxylase of Escherichia coli. Purification, properties, and pyridoxal 5 -phosphate binding site. Biochemistry, 14 (16), 3675-3681. 

Muscle glycogen phosphorylase is a dimer of two identical subunits (842 residues, 97.44 kD). Each subunit contains a pyridoxal phosphate cofactor, covalently linked as a Schiff base to Lys °. Each subunit contains an active site (at the center of the subunit) and an allosteric effector site near the subunit interface (Eigure 15.15). In addition, a regulatory phosphorylation site is located at Ser on each subunit. A glycogen-binding site on each subunit facilitates prior association of glycogen phosphorylase with its substrate and also exerts regulatory control on the enzymatic reaction. 

Pyridoxal Phosphate.—Analogues of pyridoxal and pyridoxamine 5 -phosphates have frequently been used to probe the size and shape of the active sites of a number of enzymes. For example, the apoenzyme of a tryptophanase from Bacillus alvei will bind pyridoxal 5 -phosphate as well as the 2-nor, 2 -methyl, 2 -hydroxy, 6-methyl, and A-oxide analogues.27 No analogue that has been modified at C-4 binds to the enzyme, confirming the absolute requirement for Schiff-base formation between the... 

Binding of pyridoxal phosphate to peptide PP-42 also appears to be selective for lysine 30. As was indicated by NMR spectroscopy and UV/vis experiments, only one of three potential lysine Schiff bases appeared to form. To determine the site or sites of attachment, the aldimine peptide intermediates were reduced, proteolytically cleaved, and the fragments analyzed by mass spectroscopy. This... 

Suicide Enzyme Inhibitors. Snicide substrates are irreversible enzyme inhibitors that bind covalently. The reactive anchoring group is catalytically activated by the enzyme itself through the enzyme-inhibitor complex. The enzyme thus produces its own inhibitor from an originally inactive compound, and is perceived to commit suicide. To design a substrate, the catalytic mechanism of the enzyme as well as the nature of the functional gronps at the enzyme active site must be known. Conversely, successful inhibition provides valuable information about the structure and mechanism of an enzyme. Componnds that form carbanions are especially usefnl in this regard. Pyridoxal phosphate-dependent enzymes form such carbanions readily becanse... 

It is evident, therefore, that it is the binding of canaline to the pyridoxal phosphate moiety of the enzyme rather than effective competition with ornithine for the active site that responsible for the antimetabolic properties of canaline. 

Effective concentration 65-72 entropy and 68-72 in general-acid-base catalysis 66 in nucleophilic catalysis 66 Elastase 26-30, 40 acylenzyme 27, 40 binding energies of subsites 356, 357 binding site 26-30 kinetic constants for peptide hydrolysis 357 specificity 27 Electrophiles 276 Electrophilic catalysis 61 metal ions 74-77 pyridoxal phosphate 79-82 Schiff bases 77-82 thiamine pyrophosphate 82-84 Electrostatic catalysis 61, 73, 74,498 Electrostatic effects on enzyme-substrate association rates 159-161... 

Fig. 7.8 Active site of the /3 subunit based on X-ray crystallographic results.7 The figure shows the pyridoxal phosphate Lys-87 Schiff base, the putative indole binding site at the end of the tunnel (—) that extends from the a site to the (I site, and residues selected for site directed mutagenesis. Sources Refs. 95 and 102...

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