PDBsum entry 4i1h

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protein metals links
Ligase PDB id
Protein chain
306 a.a.
_ZN ×8
Waters ×263
PDB id:
Name: Ligase
Title: Structure of parkin e3 ligase
Structure: E3 ubiquitin-protein ligase parkin. Chain: a. Fragment: r0rbr (unp residues 141-465). Synonym: parkinson juvenile disease protein 2, parkinson di protein 2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: park2, prkn. Expressed in: escherichia coli. Expression_system_taxid: 562
2.00Å     R-factor:   0.182     R-free:   0.215
Authors: J.C.Lougheed,E.Brecht,N.H.Yao
Key ref: B.E.Riley et al. (2013). Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases. Nat Commun, 4, 1982. PubMed id: 23770887 DOI: 10.1038/ncomms2982
20-Nov-12     Release date:   19-Jun-13    
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Protein chain
Pfam   ArchSchema ?
O60260  (PRKN2_HUMAN) -  E3 ubiquitin-protein ligase parkin
465 a.a.
306 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   2 terms 
  Biochemical function     ubiquitin-protein ligase activity     2 terms  


DOI no: 10.1038/ncomms2982 Nat Commun 4:1982 (2013)
PubMed id: 23770887  
Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases.
B.E.Riley, J.C.Lougheed, K.Callaway, M.Velasquez, E.Brecht, L.Nguyen, T.Shaler, D.Walker, Y.Yang, K.Regnstrom, L.Diep, Z.Zhang, S.Chiou, M.Bova, D.R.Artis, N.Yao, J.Baker, T.Yednock, J.A.Johnston.
Parkin is a RING-between-RING E3 ligase that functions in the covalent attachment of ubiquitin to specific substrates, and mutations in Parkin are linked to Parkinson's disease, cancer and mycobacterial infection. The RING-between-RING family of E3 ligases are suggested to function with a canonical RING domain and a catalytic cysteine residue usually restricted to HECT E3 ligases, thus termed 'RING/HECT hybrid' enzymes. Here we present the 1.58 Å structure of Parkin-R0RBR, revealing the fold architecture for the four RING domains, and several unpredicted interfaces. Examination of the Parkin active site suggests a catalytic network consisting of C431 and H433. In cells, mutation of C431 eliminates Parkin-catalysed degradation of mitochondria, and capture of an ubiquitin oxyester confirms C431 as Parkin's cellular active site. Our data confirm that Parkin is a RING/HECT hybrid, and provide the first crystal structure of an RING-between-RING E3 ligase at atomic resolution, providing insight into this disease-related protein.