PLP-dependent transamination template

In an aminotransferase the amino acid displaces Lys258 from PLP (transimination), Lys258 removes the α-H to give the quinonoid intermediate, reprotonation at C4′ gives the ketimine, and hydrolysis releases the α-keto acid and pyridoxamine phosphate (PMP).

Mechanism step by step

Pyridoxal phosphate is an electron sink: internal aldimine → external aldimine → quinonoid → ketimine → α-keto acid + PMP

1. Transimination – The amino group of the substrate adds to the Lys258–PLP Schiff base (internal aldimine)
2. Proton shift – The Lys258 nitrogen takes the proton from the substrate nitrogen
3. External aldimine – Lys258 is released; the substrate is now the Schiff base of PLP
4. Quinonoid – Lys258 removes the α-H; the electrons flow into the pyridinium ring (the electron sink)
5. Ketimine – The ring N pushes back; C4′ takes the proton from Lys258–H⁺
6. Hydrolysis (summarised) – Water adds to C=N⁺ and the C–N bond breaks: α-keto acid + PMP; with α-ketoglutarate the steps run backwards

Key points

• PLP is bound as a Schiff base to Lys258 (internal aldimine); the substrate swaps in by transimination to give the external aldimine.
• The protonated pyridine ring is the electron sink that stabilises the α-carbanion (quinonoid intermediate); the 3-O⁻ and 5′-phosphate (R) anchor the cofactor.
• Ping-pong (two half-reactions): amino acid + PLP → α-keto acid + PMP, then PMP + α-ketoglutarate → PLP + glutamate.
• The same aldimine chemistry, with a different bond broken at Cα, gives decarboxylation, racemisation and β-elimination (Dunathan: the bond broken lies perpendicular to the ring).

Drawn with 249 atoms, 22 arrows, 10 shapes – every one editable in MolDraw.

Sources

• Nelson & Cox, Lehninger Principles of Biochemistry, 8th ed., 2021, ch. 18 Textbook
• Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019, ch. 23 Textbook
• Braunstein & Kritzmann, Nature 1946, 158, 102 Original paper