PDBsum entry 4zyn

Ligase

PDB id: 4zyn

Contents

Protein chains

367 a.a.

385 a.a.

Ligands

SO4 ×6

Metals

_ZN ×16

Waters ×64

PDB id:

4zyn

Name:

Ligase

Title:

Crystal structure of parkin e3 ubiquitin ligase (linker deletion; delta 86-130)

Structure:

E3 ubiquitin-protein ligase parkin. Chain: a, b. Engineered: yes. Other_details: deletion 86-130

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: park2, prkn. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.54Å R-factor: 0.195 R-free: 0.235

Authors:

A.Lilov,V.Sauve,J.F.Trempe,D.Rodionov,J.Wang,K.Gehring

Key ref:

V.Sauvé et al. (2015). A Ubl/ubiquitin switch in the activation of Parkin. Embo J, 34, 2492-2505. PubMed id: 26254305 DOI: 10.15252/embj.201592237

Date:

21-May-15 Release date: 19-Aug-15

Protein chain

Q9JK66  (PRKN_RAT) -  E3 ubiquitin-protein ligase parkin from Rattus norvegicus

Seq: 465 a.a.

Struc: 367 a.a.

Protein chain

Q9JK66  (PRKN_RAT) -  E3 ubiquitin-protein ligase parkin from Rattus norvegicus

Seq: 465 a.a.

Struc: 385 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.3.2.31 - RBR-type E3 ubiquitin transferase.
• Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N₆-ubiquitinyl-L-lysine

DOI no: 10.15252/embj.201592237

Embo J 34:2492-2505 (2015)

PubMed id: 26254305

A Ubl/ubiquitin switch in the activation of Parkin.

V.Sauvé, A.Lilov, M.Seirafi, M.Vranas, S.Rasool, G.Kozlov, T.Sprules, J.Wang, J.F.Trempe, K.Gehring.

ABSTRACT

Mutations in Parkin and PINK1 cause an inherited early-onset form of Parkinson's disease. The two proteins function together in a mitochondrial quality control pathway whereby PINK1 accumulates on damaged mitochondria and activates Parkin to induce mitophagy. How PINK1 kinase activity releases the auto-inhibited ubiquitin ligase activity of Parkin remains unclear. Here, we identify a binding switch between phospho-ubiquitin (pUb) and the ubiquitin-like domain (Ubl) of Parkin as a key element. By mutagenesis and SAXS, we show that pUb binds to RING1 of Parkin at a site formed by His302 and Arg305. pUb binding promotes disengagement of the Ubl from RING1 and subsequent Parkin phosphorylation. A crystal structure of Parkin Δ86-130 at 2.54 Å resolution allowed the design of mutations that specifically release the Ubl domain from RING1. These mutations mimic pUb binding and promote Parkin phosphorylation. Measurements of the E2 ubiquitin-conjugating enzyme UbcH7 binding to Parkin and Parkin E3 ligase activity suggest that Parkin phosphorylation regulates E3 ligase activity downstream of pUb binding.