9IIT

Full length structure of FKP in complex with GTP and GDP

9IIT の概要

• エントリーDOI: 10.2210/pdb9iit/pdb
• 関連するPDBエントリー: 9iip 9iis
• 分子名称: L-fucokinase/L-fucose-1-P guanylyltransferase, GUANOSINE-5'-TRIPHOSPHATE, FORMIC ACID, ... (8 entities in total)
• 機能のキーワード: fucose, atp, gtp, kinase, pyrophosphorylase, transferase
• 由来する生物種: Bacteroides fragilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 218603.64

構造登録者

Ko, T.P.,Lin, S.W.,Hsu, M.F.,Lin, C.H. (登録日: 2024-06-21, 公開日: 2025-03-05, 最終更新日: 2025-04-09)

主引用文献

Lin, S.W.,Ko, T.P.,Chiang, H.Y.,Wu, C.G.,Hsu, M.F.,Wang, A.H.,Lin, C.H.
Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase.
J.Biol.Chem., 301:108344-108344, 2025

PubMed Abstract: The bifunctional l-fucokinase/GDP-β-l-fucose pyrophosphorylase (FKP) from Bacteroides fragilis catalyzes the conversion from l-fucose to GDP-β-l-fucose. The reaction product, representing the activated form of l-fucose, is used by all l-fucosyltransferases to incorporate l-fucose. Herein, we report the first X-ray crystal structures of FKP in complex with substrate-product, leading to the dissection of both activity domains and corresponding catalytic mechanisms. The full-length FKP (FKP-FL, 949 amino acids) exists as a tetramer in solution, but the individually prepared N-terminal domain (FKP-NTD corresponding to the sequence 1-496, also containing a SUMO tag) and C-terminal domain (FKP-CTD, the sequence 519-949) form a monomer and a dimer, respectively. FKP-NTD has a single α/β domain and a β-helix-containing domain, whereas FKP-CTD folds into two α/β domains and the linker comprises three α-helices. The β-l-fucose-1-phosphate (fucose-1-P) and GTP bound separately to the active sites of fucokinase (located at FKP-CTD) and pyrophosphorylase (FKP-NTD), and a third nucleotide-binding site is adjacent to the β-helix (also in FKP-NTD). Furthermore, Asp762 was proposed to serve as the general base in the reaction of fucokinase, to deprotonate the C1-OH of fucose in the nucleophilic attack to γ-phosphate of ATP, resulting in the formation of fucose-1-P. At the same time, Arg592 and magnesium ion stabilize the developing negative charge in the leaving group (ADP). Subsequently, in the pyrophosphorylase-catalyzed reaction, the Lys187 side chain facilitates the nucleophilic attack of fucose-1-P toward GTP, leading to the formation of GDP-fucose.

PubMed: 39993526
DOI: 10.1016/j.jbc.2025.108344

実験手法

X-RAY DIFFRACTION (2.3 Å)