PDBsum entry 5d0i

Metal binding protein

PDB id: 5d0i

Contents

Protein chains

62 a.a.

51 a.a.

Ligands

SO4

Metals

_ZN ×4

Waters ×65

PDB id:

5d0i

Name:

Metal binding protein

Title:

Structure of ring finger protein 165

Structure:

Ring finger protein 165. Chain: a, b. Fragment: unp residues 255-346. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf165. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.175 R-free: 0.200

Authors:

J.D.Wright,C.L.Day,P.D.Mace

Key ref:

J.D.Wright et al. (2016). Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Nat Struct Biol, 23, 45-52. PubMed id: 26656854 DOI: 10.1038/nsmb.3142

Date:

03-Aug-15 Release date: 09-Dec-15

Protein chain

Q6ZSG1  (RN165_HUMAN) -  E3 ubiquitin-protein ligase ARK2C from Homo sapiens

Seq: 346 a.a.

Struc: 62 a.a.

Protein chain

Q6ZSG1  (RN165_HUMAN) -  E3 ubiquitin-protein ligase ARK2C from Homo sapiens

Seq: 346 a.a.

Struc: 51 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1038/nsmb.3142

Nat Struct Biol 23:45-52 (2016)

PubMed id: 26656854

Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.

J.D.Wright, P.D.Mace, C.L.Day.

ABSTRACT

RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.