PDBsum entry 5d0k

Ligase

PDB id: 5d0k

Contents

Protein chains

148 a.a.

69 a.a.

76 a.a.

Metals

_ZN ×8

Waters ×3

PDB id:

5d0k

Name:

Ligase

Title:

Structure of ube2d2:rnf165:ub complex

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a, d, g, j. Synonym: ubiquitin carrier protein d2,ubiquitin-conjugating enzyme e2(17)kb 2,ubiquitin-conjugating enzyme e2-17 kda 2,ubiquitin-protein ligase d2,p53-regulated ubiquitin-conjugating enzyme 1. Engineered: yes. Mutation: yes. Ring finger protein 165. Chain: c, f, i, l.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d2, pubc1, ubc4, ubc5b, ubch4, ubch5b. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rnf165. Gene: ubb. Expression_system_taxid: 562

Resolution:

2.65Å R-factor: 0.194 R-free: 0.238

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 chains

P62837  (UB2D2_HUMAN) -  Ubiquitin-conjugating enzyme E2 D2 from Homo sapiens

Seq: 147 a.a.

Struc: 148 a.a.*

Protein chains

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

Seq: 346 a.a.

Struc: 69 a.a.

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, D, G, J: E.C.2.3.2.23 - E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine
• Enzyme class 3: Chains A, D, G, J: E.C.2.3.2.24 - (E3-independent) E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N₆- monoubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 4: Chains B, E, H, K: E.C.?
• Enzyme class 5: Chains C, F, I, L: 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

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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.