PDBsum entry 5aiu

Ligase/signaling protein

PDB id: 5aiu

Contents

Protein chains

123 a.a.

150 a.a.

76 a.a.

Ligands

EDO ×6

Metals

_ZN ×4

Waters ×33

PDB id:

5aiu

Name:

Ligase/signaling protein

Title:

A complex of rnf4-ring domain, ubc13-ub (isopeptide crosslink)

Structure:

E3 ubiquitin-protein ligase rnf4. Chain: a. Fragment: ring domain, unp residues 131-194,131-194. Synonym: ring finger protein 4, small nuclear ring finger protein, protein snurf, "ring domain, ubc13". Engineered: yes. Mutation: yes. Other_details: the ring domain is duplicated but as a fused dimer. That is the sequence of the ring domain from rnf4 (residues 131 to

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562

Resolution:

2.21Å R-factor: 0.219 R-free: 0.255

Authors:

E.Branigan,J.H.Naismith

Key ref:

E.Branigan et al. (2015). Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains. Nat Struct Biol, 22, 597-602. PubMed id: 26148049 DOI: 10.1038/nsmb.3052

Date:

17-Feb-15 Release date: 08-Jul-15

Protein chain

O88846  (RNF4_RAT) -  E3 ubiquitin-protein ligase RNF4 from Rattus norvegicus

Seq: 194 a.a.

Struc: 123 a.a.

Protein chains

P61088  (UBE2N_HUMAN) -  Ubiquitin-conjugating enzyme E2 N from Homo sapiens

Seq: 152 a.a.

Struc: 150 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: Chains B, E: 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 4: Chains C, F: E.C.?

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.3052

Nat Struct Biol 22:597-602 (2015)

PubMed id: 26148049

Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains.

E.Branigan, A.Plechanovová, E.G.Jaffray, J.H.Naismith, R.T.Hay.

ABSTRACT

RING E3 ligase-catalyzed formation of K63-linked ubiquitin chains by the Ube2V2-Ubc13 E2 complex is required in many important biological processes. Here we report the structure of the RING-domain dimer of rat RNF4 in complex with a human Ubc13∼Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with K63 in a position favorable for attack on the linkage between Ubc13 and the donor (second) ubiquitin held in the active 'folded back' conformation by the RING domain of RNF4. We verified the interfaces identified in the structure by in vitro ubiquitination assays of site-directed mutants. To our knowledge, this represents the first view of synthesis of K63-linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase-mediated catalysis.