2EFC

Ara7-GDP/AtVps9a

2EFC の概要

• エントリーDOI: 10.2210/pdb2efc/pdb
• 関連するPDBエントリー: 2efe 2efh 2fed
• 分子名称: Similarity to vacuolar protein sorting-associated protein VPS9, Small GTP-binding protein-like, GUANOSINE-5'-DIPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: gef, gtpase, vps9, rab5, nucleotide, transport protein
• 由来する生物種: Arabidopsis thaliana (thale cress); 詳細
• 細胞内の位置: Early endosome membrane: Q9SN68
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 100997.90

構造登録者

Uejima, T.,Ihara, K.,Goh, T.,Ito, E.,Sunada, M.,Ueda, T.,Nakano, A.,Wakatsuki, S. (登録日: 2007-02-22, 公開日: 2008-02-26, 最終更新日: 2024-04-03)

主引用文献

Uejima, T.,Ihara, K.,Goh, T.,Ito, E.,Sunada, M.,Ueda, T.,Nakano, A.,Wakatsuki, S.
GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
J.Biol.Chem., 285:36689-36697, 2010

PubMed Abstract: Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7·VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP β-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP β-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.

PubMed: 20833725
DOI: 10.1074/jbc.M110.152132

実験手法

X-RAY DIFFRACTION (2.09 Å)