2GRR

Crystal Structure of human RanGAP1-Ubc9-D127S

Summary for 2GRR

• Entry DOI: 10.2210/pdb2grr/pdb
• Related: 2GRN 2GRO 2GRP 2GRQ
• Descriptor: Ubiquitin-conjugating enzyme E2 I, Ran GTPase-activating protein 1 (3 entities in total)
• Functional Keywords: ubiquitin, conjugation, small ubiquitin like modifer, smt3, ligase
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P63279; Cytoplasm: P46060
• Total number of polymer chains: 2
• Total formula weight: 36744.43

Authors

Yunus, A.A.,Lima, C.D. (deposition date: 2006-04-24, release date: 2006-05-30, Last modification date: 2024-02-14)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.3 Å)