PDBsum entry 8eb0

Ligase

PDB id: 8eb0

Contents

Protein chains

255 a.a.

146 a.a.

76 a.a.

Ligands

SO4 ×3

Metals

_ZN ×7

PDB id:

8eb0

Name:

Ligase

Title:

Rnf216/e2-ub/ub transthiolation complex

Structure:

E3 ubiquitin-protein ligase rnf216. Chain: a. Synonym: ring finger protein 216,ring-type e3 ubiquitin transferase rnf216,triad domain-containing protein 3,ubiquitin-conjugating enzyme 7-interacting protein 1,zinc finger protein inhibiting nf-kappa-b. Engineered: yes. Mutation: yes. Other_details: s719 is phosphorylated. Ubiquitin-conjugating enzyme e2 l3.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf216, triad3, ubce7ip1, zin. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ube2l3, ubce7, ubch7. Gene: ubc. Expression_system_taxid: 469008

Resolution:

3.03Å R-factor: 0.306 R-free: 0.339

Authors:

T.R.Cotton,X.S.Wang,B.C.Lechtenberg

Key ref:

X.S.Wang et al. (2023). The unifying catalytic mechanism of the ring-Between- Ubiquitin ligase family.. Nat commun, 14, 168. PubMed id: 36631489

Date:

30-Aug-22 Release date: 18-Jan-23

Protein chain

Q9NWF9  (RN216_HUMAN) -  E3 ubiquitin-protein ligase RNF216 from Homo sapiens

Seq: 866 a.a.

Struc: 255 a.a.*

Protein chain

P68036  (UB2L3_HUMAN) -  Ubiquitin-conjugating enzyme E2 L3 from Homo sapiens

Seq: 154 a.a.

Struc: 146 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain A: 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
• Enzyme class 3: Chain B: 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

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.