4II2

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg

Summary for 4II2

• Entry DOI: 10.2210/pdb4ii2/pdb
• Related: 4II3
• Descriptor: Ubiquitin-activating enzyme E1 1, Ubiquitin-60S ribosomal protein L40, Ubiquitin-conjugating enzyme E2 4, ... (9 entities in total)
• Functional Keywords: ubiquitin, e1, e2, uba1, ubc4, conformational change, thioester, adenylation, thioester transfer (transthioesterification), atp-binding, rossmann-like fold, ubiquitin-like fold, ligase activity, atp/mg binding, ubiquitin e2 binding, ubiquitination, nucleus, ligase
• Biological source: Schizosaccharomyces pombe (Fission yeast); More
• Cellular location: Cytoplasm: O94609; Ubiquitin: Cytoplasm . 60S ribosomal protein L40: Cytoplasm : P0CH07
• Total number of polymer chains: 3
• Total formula weight: 141137.09

Authors

Olsen, S.K.,Lima, C.D. (deposition date: 2012-12-19, release date: 2013-02-13, Last modification date: 2024-11-06)

Primary citation

Olsen, S.K.,Lima, C.D.
Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.
Mol.Cell, 49:884-896, 2013

PubMed Abstract: Ubiquitin (Ub) conjugation is initiated by an E1 enzyme that catalyzes carboxy-terminal Ub adenylation, thioester bond formation to a catalytic cysteine in the E1 Cys domain, and thioester transfer to a catalytic cysteine in E2 conjugating enzymes. How the E1 and E2 active sites come together during thioester transfer and how Ub E1 interacts with diverse Ub E2s remains unclear. Here we present a crystal structure of a Ub E1-E2(Ubc4)/Ub/ATP·Mg complex that was stabilized by induction of a disulfide bond between the E1 and E2 active sites. The structure reveals combinatorial recognition of the E2 by the E1 ubiquitin-fold domain (UFD) and Cys domain and mutational analysis, coupled with thioester transfer assays with E1, Ubc4, and other Ub E2s, show that both interfaces are important for thioester transfer. Comparison to a Ub E1/Ub/ATP·Mg structure reveals conformational changes in the E1 that bring the E1 and E2 active sites together.

PubMed: 23416107
DOI: 10.1016/j.molcel.2013.01.013

Experimental method

X-RAY DIFFRACTION (2.2 Å)