3O0D

Crystal structure of Lip2 lipase from Yarrowia lipolytica at 1.7 A resolution

3O0D の概要

• エントリーDOI: 10.2210/pdb3o0d/pdb
• 分子名称: Triacylglycerol lipase, 2-acetamido-2-deoxy-beta-D-glucopyranose, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (6 entities in total)
• 機能のキーワード: alpha/beta-hydrolase, lipase, lipids binding, glycosylation, extracellular, hydrolase
• 由来する生物種: Yarrowia lipolytica (Candida lipolytica)
• タンパク質・核酸の鎖数: 7
• 化学式量合計: 239288.90

構造登録者

Bordes, F.,Tranier, S.,Mourey, L.,Marty, A. (登録日: 2010-07-19, 公開日: 2010-11-24, 最終更新日: 2024-11-20)

主引用文献

Bordes, F.,Barbe, S.,Escalier, P.,Mourey, L.,Andre, I.,Marty, A.,Tranier, S.
Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase.
Biophys.J., 99:2225-2234, 2010

PubMed Abstract: We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.

PubMed: 20923657
DOI: 10.1016/j.bpj.2010.07.040

実験手法

X-RAY DIFFRACTION (1.7 Å)