Observation of an E2 (Ubc9)-homodimer by crystallography

• Published in: Data in brief Vol. 7; pp. 195 - 200
• Main Authors: Alontaga, Aileen Y., Ambaye, Nigus D., Li, Yi-Jia, Vega, Ramir, Chen, Chih-Hong, Bzymek, Krzysztof P., Williams, John C., Hu, Weidong, Chen, Yuan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.06.2016; Elsevier
• Subjects: crystal structure; crystallography; Data; Modifications; Poly-SUMO chain; RWD; site-directed mutagenesis; SUMO; Ubc9; Ubiquitin; Ubiquitin-like; ubiquitin-protein ligase; Ubiquitin; Modifications; Ubiquitin-like; SUMO; Ubc9; E1; Poly-SUMO chain; RWD
• ISSN: 2352-3409; 2352-3409
• DOI: 10.1016/j.dib.2016.02.015

Post-translational modifications by the small ubiquitin-like modifiers (SUMO), in particular the formation of poly-SUMO-2 and -3 chains, regulates essential cellular functions and its aberration leads to life-threatening diseases (Geoffroy and Hay, 2009) [1]. It was shown previously that the non-covalent interaction between SUMO and the conjugating enzyme (E2) for SUMO, known as Ubc9, is required for poly-SUMO-2/3 chain formation (Knipscheer et al., 2007) [2]. However, the structure of SUMO-Ubc9 non-covalent complex, by itself, could not explain how the poly-SUMO-2/3 chain forms and consequently a Ubc9 homodimer, although never been observed, was proposed for poly-SUMO-2/3 chain formation (Knipscheer et al., 2007) [2]. Here, we solved the crystal structure of a heterotrimer containing a homodimer of Ubc9 and the RWD domain from RWDD3. The asymmetric Ubc9 homodimer is mediated by the N-terminal region of one Ubc9 molecule and a surface near the catalytic Cys of the second Ubc9 molecule (Fig. 1A). This N-terminal surface of Ubc9 that is involved in the homodimer formation also interacts with the RWD domain, the ubiquitin-fold domain of the SUMO activating enzyme (E1), SUMO, and the E3 ligase, RanBP2 (Knipscheer et al., 2007; Tong et al.. 1997; Tatham et al., 2005; Reverter and Lima, 2005; Capili and Lima, 2007; Wang et al., 2009, 2010; Wang and Chen, 2010; Alontaga et al., 2015) [2–10]. The existence of the Ubc9 homodimer in solution is supported by previously published solution NMR studies of rotational correlation time and chemical shift perturbation (Alontaga et al., 2015; Yuan et al., 1999) [10,11]. Site-directed mutagenesis and biochemical analysis suggests that this dimeric arrangement of Ubc9 is likely important for poly-SUMO chain formation (Fig. 1B and C). The asymmetric Ubc9 homodimer described for the first time in this work could provide the critical missing link in the poly-SUMO chain formation mechanism. The data presented here are related to the research article entitled, “RWD domain as an E2 (Ubc9) interaction module” (Alontaga et al., 2015) [10]. The data of the crystal structure has been deposited to RCSB protein data bank with identifier: 4Y1L.