4Y1L

Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation

Summary for 4Y1L

• Entry DOI: 10.2210/pdb4y1l/pdb
• Descriptor: SUMO-conjugating enzyme UBC9, RWD domain-containing protein 3 (3 entities in total)
• Functional Keywords: ubc9, rwd, sumoylation, homodimer, sumo, ligase-nuclear protein complex, ligase/nuclear protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 48922.31

Authors

Aileen, Y.A.,Ambaye, N.D.,Li, Y.J.,Vega, R.,Bzymek, K.,Williams, J.C.,Hu, W.,Chen, Y. (deposition date: 2015-02-08, release date: 2015-05-06, Last modification date: 2024-02-28)

Primary citation

Alontaga, A.Y.,Ambaye, N.D.,Li, Y.J.,Vega, R.,Chen, C.H.,Bzymek, K.P.,Williams, J.C.,Hu, W.,Chen, Y.
RWD Domain as an E2 (Ubc9)-Interaction Module.
J.Biol.Chem., 290:16550-16559, 2015

PubMed Abstract: An RWD domain is a well conserved domain found through bioinformatic analysis of the human proteome sequence; however, its function has been unknown. Ubiquitin-like modifications require the catalysis of three enzymes generally known as E1, E2, and E3. We solved the crystal structure of the E2 for the small ubiquitin-like modifiers (SUMO) in complex with an RWD domain and confirmed the structure using solution NMR analysis. The binding surface of RWD on Ubc9 is located near the N terminus of Ubc9 that is known to be involved in noncovalent binding of the proteins in the conjugation machinery, including a domain of E1, SUMO, and an E3 ligase. NMR data indicate that the RWD domain does not bind to SUMO and E1. The interaction between RWD and Ubc9 has a Kd of 32 ± 4 μM. Consistent with the structure and binding affinity and in contrast to a previous report, the RWD domain and RWDD3 have minimal effects on global SUMOylation. The structural and biochemical information presented here forms the basis for further investigation of the functions of RWD-containing proteins.

PubMed: 25918163
DOI: 10.1074/jbc.M115.644047

Experimental method

X-RAY DIFFRACTION (2.7 Å)