3PT3

Crystal structure of the C-terminal lobe of the human UBR5 HECT domain

Summary for 3PT3

• Entry DOI: 10.2210/pdb3pt3/pdb
• Descriptor: E3 ubiquitin-protein ligase UBR5 (2 entities in total)
• Functional Keywords: ubr5, edd, hhyd, mixed alpha-beta fold, ubiquitin ligase, ligase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: O95071
• Total number of polymer chains: 2
• Total formula weight: 27037.06

Authors

Matta-Camacho, E.,Kozlov, G.,Menade, M.,Gehring, K. (deposition date: 2010-12-02, release date: 2012-01-25, Last modification date: 2023-09-06)

Primary citation

Matta-Camacho, E.,Kozlov, G.,Menade, M.,Gehring, K.
Structure of the HECT C-lobe of the UBR5 E3 ubiquitin ligase.
Acta Crystallogr.,Sect.F, 68:1158-1163, 2012

PubMed Abstract: UBR5 ubiquitin ligase (also known as EDD, Rat100 or hHYD) is a member of the E3 protein family of HECT (homologous to E6-AP C-terminus) ligases as it contains a C-terminal HECT domain. In ubiquitination cascades involving E3s of the HECT class, ubiquitin is transferred from an associated E2 ubiquitin-conjugating enzyme to the acceptor cysteine of the HECT domain, which consists of structurally distinct N- and C-lobes connected by a flexible linker. Here, the high-resolution crystal structure of the C-lobe of the HECT domain of human UBR5 is presented. The structure reveals important features that are unique compared with other HECT domains. In particular, a distinct four-residue insert in the second helix elongates this helix, resulting in a strikingly different orientation of the preceding loop. This protruding loop is likely to contribute to specificity towards the E2 ubiquitin-conjugating enzyme UBCH4, which is an important functional partner of UBR5. Ubiquitination assays showed that the C-lobe of UBR5 is able to form a thioester-linked E3-ubiquitin complex, although it does not physically interact with UBCH4 in NMR experiments. This study contributes to a better understanding of UBR5 ubiquitination activity.

PubMed: 23027739
DOI: 10.1107/S1744309112036937

Experimental method

X-RAY DIFFRACTION (1.97 Å)