8IKM image
Deposition Date 2023-02-28
Release Date 2024-09-11
Last Version Date 2024-10-09
Entry Detail
PDB ID:
8IKM
Keywords:
Title:
Trans complex of phospho parkin
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.92 Å
R-Value Free:
0.23
R-Value Work:
0.20
Space Group:
P 32 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase parkin
Gene (Uniprot):PRKN
Mutagens:Q347C
Chain IDs:A
Chain Length:247
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin
Gene (Uniprot):UBA52
Chain IDs:B
Chain Length:75
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase parkin
Gene (Uniprot):PRKN
Chain IDs:C
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP B SER modified residue
Primary Citation
Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans.
Elife 13 ? ? (2024)
PMID: 39221915 DOI: 10.7554/eLife.96699

Abstact

Loss-of-function Parkin mutations lead to early-onset of Parkinson's disease. Parkin is an auto-inhibited ubiquitin E3 ligase activated by dual phosphorylation of its ubiquitin-like (Ubl) domain and ubiquitin by the PINK1 kinase. Herein, we demonstrate a competitive binding of the phospho-Ubl and RING2 domains towards the RING0 domain, which regulates Parkin activity. We show that phosphorylated Parkin can complex with native Parkin, leading to the activation of autoinhibited native Parkin in trans. Furthermore, we show that the activator element (ACT) of Parkin is required to maintain the enzyme kinetics, and the removal of ACT slows the enzyme catalysis. We also demonstrate that ACT can activate Parkin in trans but less efficiently than when present in the cis molecule. Furthermore, the crystal structure reveals a donor ubiquitin binding pocket in the linker connecting REP and RING2, which plays a crucial role in Parkin activity.

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Primary Citation of related structures