2GRQ

Crystal Structure of human RanGAP1-Ubc9-D127A

2GRQ の概要

• エントリーDOI: 10.2210/pdb2grq/pdb
• 関連するPDBエントリー: 2GRN 2GRO 2GRP 2GRR
• 分子名称: Ubiquitin-conjugating enzyme E2 I, Ran GTPase-activating protein 1 (3 entities in total)
• 機能のキーワード: ubiquitin, conjugation, small ubiquitin like modifer, smt3, ligase
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P63279; Cytoplasm: P46060
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 36728.43

構造登録者

Yunus, A.A.,Lima, C.D. (登録日: 2006-04-24, 公開日: 2006-05-30, 最終更新日: 2024-02-14)

主引用文献

Yunus, A.A.,Lima, C.D.
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
Nat.Struct.Mol.Biol., 13:491-499, 2006

PubMed Abstract: E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.

PubMed: 16732283
DOI: 10.1038/nsmb1104

実験手法

X-RAY DIFFRACTION (1.7 Å)