1YRV

Novel Ubiquitin-Conjugating Enzyme

Summary for 1YRV

• Entry DOI: 10.2210/pdb1yrv/pdb
• Descriptor: ubiquitin-conjugating ligase MGC351130 (2 entities in total)
• Functional Keywords: structural genomics consortium; sgc; ubiquitin; ubiquitin-conjugating enzyme; ligase, ligase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 19452.15

Authors

Walker, J.R.,Choe, J.,Avvakumov, G.V.,Newman, E.M.,MacKenzie, F.,Sundstrom, M.,Arrowsmith, C.,Edwards, A.,Bochkarev, A.,Dhe-Paganon, S.,Structural Genomics Consortium (SGC) (deposition date: 2005-02-04, release date: 2005-03-22, Last modification date: 2023-08-23)

Primary citation

Sheng, Y.,Hong, J.H.,Doherty, R.,Srikumar, T.,Shloush, J.,Avvakumov, G.V.,Walker, J.R.,Xue, S.,Neculai, D.,Wan, J.W.,Kim, S.K.,Arrowsmith, C.H.,Raught, B.,Dhe-Paganon, S.
A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Mol Cell Proteomics, 11:329-341, 2012

PubMed Abstract: Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.

PubMed: 22496338
DOI: 10.1074/mcp.O111.013706

Experimental method

X-RAY DIFFRACTION (2.18 Å)