4AP4

Rnf4 - ubch5a - ubiquitin heterotrimeric complex

Summary for 4AP4

• Entry DOI: 10.2210/pdb4ap4/pdb
• Related: 2C4P 2YHO
• Descriptor: E3 UBIQUITIN LIGASE RNF4, UBIQUITIN-CONJUGATING ENZYME E2 D1, UBIQUITIN C, ... (5 entities in total)
• Functional Keywords: ligase-signalling protein complex, chimera, ligase/signalling protein
• Biological source: RATTUS NORVEGICUS (NORWAY RAT); More
• Total number of polymer chains: 5
• Total formula weight: 67075.31

Authors

Plechanovova, A.,Hay, R.T.,Tatham, M.H.,Jaffray, E.,Naismith, J.H. (deposition date: 2012-03-30, release date: 2012-07-25, Last modification date: 2023-12-20)

Primary citation

Plechanovova, A.,Jaffray, E.,Tatham, M.H.,Naismith, J.H.,Hay, R.T.
Structure of a Ring E3 Ligase and Ubiquitin-Loaded E2 Primed for Catalysis
Nature, 489:115-, 2012

PubMed Abstract: Ubiquitin modification is mediated by a large family of specificity determining ubiquitin E3 ligases. To facilitate ubiquitin transfer, RING E3 ligases bind both substrate and a ubiquitin E2 conjugating enzyme linked to ubiquitin via a thioester bond, but the mechanism of transfer has remained elusive. Here we report the crystal structure of the dimeric RING domain of rat RNF4 in complex with E2 (UbcH5A) linked by an isopeptide bond to ubiquitin. While the E2 contacts a single protomer of the RING, ubiquitin is folded back onto the E2 by contacts from both RING protomers. The carboxy-terminal tail of ubiquitin is locked into an active site groove on the E2 by an intricate network of interactions, resulting in changes at the E2 active site. This arrangement is primed for catalysis as it can deprotonate the incoming substrate lysine residue and stabilize the consequent tetrahedral transition-state intermediate.

PubMed: 22842904
DOI: 10.1038/NATURE11376

Experimental method

X-RAY DIFFRACTION (2.21 Å)