4II3
Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg
Summary for 4II3
| Entry DOI | 10.2210/pdb4ii3/pdb |
| Related | 4II2 |
| Descriptor | Ubiquitin-activating enzyme E1 1, Ubiquitin-60S ribosomal protein L40, MAGNESIUM ION, ... (6 entities in total) |
| Functional Keywords | rossmann-like fold, ubiquitin-like fold, ubiquitin activating enzyme activity, atp binding, ligase activity, atp/mg binding, ubiquitin e2 binding, 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 | 4 |
| Total formula weight | 246520.72 |
| Authors | Olsen, S.K.,Lima, C.D. (deposition date: 2012-12-19, release date: 2013-02-13, Last modification date: 2023-09-20) |
| 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 Cited by 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: 23416107DOI: 10.1016/j.molcel.2013.01.013 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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