4KCU

Pyruvate kinase (PYK) from Trypanosoma brucei soaked with D-Malate

4KCU の概要

• エントリーDOI: 10.2210/pdb4kcu/pdb
• 関連するPDBエントリー: 4HYV 4HYW 4KCT 4KCV 4KCW
• 分子名称: Pyruvate kinase 1, MAGNESIUM ION, POTASSIUM ION, ... (6 entities in total)
• 機能のキーワード: pyruvate kinase, decarboxylase, transferase
• 由来する生物種: Trypanosoma brucei brucei
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 110154.33

構造登録者

Zhong, W.,Morgan, H.P.,McNae, I.W.,Michels, P.A.M.,Fothergill-Gilmore, L.A.,Walkinshaw, M.D. (登録日: 2013-04-24, 公開日: 2014-01-08, 最終更新日: 2024-02-28)

主引用文献

Zhong, W.,Morgan, H.P.,Nowicki, M.W.,McNae, I.W.,Yuan, M.,Bella, J.,Michels, P.A.,Fothergill-Gilmore, L.A.,Walkinshaw, M.D.
Pyruvate kinases have an intrinsic and conserved decarboxylase activity.
Biochem.J., 458:301-311, 2014

PubMed Abstract: The phosphotransfer mechanism of PYKs (pyruvate kinases) has been studied in detail, but the mechanism of the intrinsic decarboxylase reaction catalysed by PYKs is still unknown. 1H NMR was used in the present study to follow OAA (oxaloacetate) decarboxylation by trypanosomatid and human PYKs confirming that the decarboxylase activity is conserved across distantly related species. Crystal structures of TbPYK (Trypanosoma brucei PYK) complexed with the product of the decarboxylase reaction (pyruvate), and a series of substrate analogues (D-malate, 2-oxoglutarate and oxalate) show that the OAA analogues bind to the kinase active site with similar binding modes, confirming that both decarboxylase and kinase activities share a common site for substrate binding and catalysis. Decarboxylation of OAA as monitored by NMR for TbPYK has a relatively low turnover with values of 0.86 s-1 and 1.47 s-1 in the absence and presence of F26BP (fructose 2,6-bisphosphate) respectively. Human M1PYK (M1 isoform of PYK) has a measured turnover value of 0.50 s-1. The X-ray structures explain why the decarboxylation activity is specific for OAA and is not general for α-oxo acid analogues. Conservation of the decarboxylase reaction across divergent species is a consequence of piggybacking on the conserved kinase mechanism which requires a stabilized enol intermediate.

PubMed: 24328825
DOI: 10.1042/BJ20130790

実験手法

X-RAY DIFFRACTION (2.35 Å)