3L1Z

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme

Summary for 3L1Z

• Entry DOI: 10.2210/pdb3l1z/pdb
• Related: 3L1X 3L1Y
• Descriptor: Ubiquitin-conjugating enzyme E2 D3, Ubiquitin conjugation factor E4 B (3 entities in total)
• Functional Keywords: e4b, ufd2a, ubch5c, u-box ubiquitin ligase, e2 ubiquitin conjugating enzyme, ubl conjugation pathway, ligase
• Biological source: Homo sapiens (human); More
• Cellular location: Cell membrane; Peripheral membrane protein: P61077; Cytoplasm (By similarity): O95155
• Total number of polymer chains: 2
• Total formula weight: 29547.58

Authors

Benirschke, R.,Thompson, J.R.,Mer, G. (deposition date: 2009-12-14, release date: 2010-05-05, Last modification date: 2023-09-06)

Primary citation

Benirschke, R.C.,Thompson, J.R.,Nomine, Y.,Wasielewski, E.,Juranic, N.,Macura, S.,Hatakeyama, S.,Nakayama, K.I.,Botuyan, M.V.,Mer, G.
Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4.
Structure, 18:955-965, 2010

PubMed Abstract: Human E4B, also called UFD2a, is a U box-containing protein that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor. E4B is thought to participate in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. The U box domain is an anchor site for E2 ubiquitin-conjugating enzymes, but little is known of the binding mechanism. Using X-ray crystallography and NMR spectroscopy, we determined the structures of E4B U box free and bound to UbcH5c and Ubc4 E2s. Whereas previously characterized U box domains are homodimeric, we show that E4B U box is a monomer stabilized by a network of hydrogen bonds identified from scalar coupling measurements. These structural studies, complemented by calorimetry- and NMR-based binding assays, suggest an allosteric regulation of UbcH5c and Ubc4 by E4B U box and provide a molecular basis to understand how the ubiquitylation machinery involving E4B assembles.

PubMed: 20696396
DOI: 10.1016/j.str.2010.04.017

Experimental method

X-RAY DIFFRACTION (3.17 Å)