5D1K: Crystal Structure Of Ubch5b In Complex With The Ring-u5br Fragment Of Ao7

Citation:
Abstract
RING proteins constitute the largest class of E3 ubiquitin ligases. Unlike most RINGs, AO7 (RNF25) binds the E2 ubiquitin-conjugating enzyme, UbcH5B (UBE2D2), with strikingly high affinity. We have defined, by co-crystallization, the distinctive means by which AO7 binds UbcH5B. AO7 contains a structurally unique UbcH5B binding region (U5BR) that is connected by an 11-amino acid linker to its RING domain, forming a clamp surrounding the E2. The U5BR interacts extensively with a region of UbcH5B that is distinct from both the active site and the RING-interacting region, referred to as the backside of the E2. An apparent paradox is that the high-affinity binding of the AO7 clamp to UbcH5B, which is dependent on the U5BR, decreases the rate of ubiquitination. We establish that this is a consequence of blocking the stimulatory, non-covalent, binding of ubiquitin to the backside of UbcH5B. Interestingly, when non-covalent backside ubiquitin binding cannot occur, the AO7 clamp now enhances the rate of ubiquitination. The high-affinity binding of the AO7 clamp to UbcH5B has also allowed for the co-crystallization of previously described and functionally important RING mutants at the RING-E2 interface. We show that mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface.
PDB ID: 5D1KDownload
MMDB ID: 133754
PDB Deposition Date: 2013/10/8
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 1.78  Å
Source Organism:
Similar Structures:
Biological Unit for 5D1K: dimeric; determined by author and by software (PISA)
Molecular Components in 5D1K
Label Count Molecule
Proteins (2 molecules)
1
Ubiquitin-conjugating Enzyme E2 D2(Gene symbol: UBE2D2)
Molecule annotation
1
E3 Ubiquitin-protein Ligase Rnf25(Gene symbol: RNF25)
Molecule annotation
Chemicals (7 molecules)
1
3
2
1
3
1
4
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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