2QHO

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin

Summary for 2QHO

• Entry DOI: 10.2210/pdb2qho/pdb
• Descriptor: Ubiquitin, E3 ubiquitin-protein ligase EDD1 (3 entities in total)
• Functional Keywords: protein-protein complex, protein binding-ligase complex, protein binding/ligase
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: O95071
• Total number of polymer chains: 8
• Total formula weight: 57585.40

Authors

Kozlov, G.,Gehring, K. (deposition date: 2007-07-02, release date: 2007-09-25, Last modification date: 2023-08-30)

Primary citation

Kozlov, G.,Nguyen, L.,Lin, T.,De Crescenzo, G.,Park, M.,Gehring, K.
Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD.
J.Biol.Chem., 282:35787-35795, 2007

PubMed Abstract: EDD (or HYD) is an E3 ubiquitin ligase in the family of HECT (homologous to E6-AP C terminus) ligases. EDD contains an N-terminal ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Here, we use isothermal titration calorimetry (ITC), NMR titrations, and pull-down assays to show that the EDD UBA domain binds ubiquitin. The 1.85 A crystal structure of the complex with ubiquitin reveals the structural basis of ubiquitin recognition by UBA helices alpha1 and alpha3. The structure shows a larger number of intermolecular hydrogen bonds than observed in previous UBA/ubiquitin complexes. Two of these involve ordered water molecules. The functional importance of residues at the UBA/ubiquitin interface was confirmed using site-directed mutagenesis. Surface plasmon resonance (SPR) measurements show that the EDD UBA domain does not have a strong preference for polyubiquitin chains over monoubiquitin. This suggests that EDD binds to monoubiquitinated proteins, which is consistent with its involvement in DNA damage repair pathways.

PubMed: 17897937
DOI: 10.1074/jbc.M705655200

Experimental method

X-RAY DIFFRACTION (1.85 Å)