PDBsum entry 4p5o

Ligase

PDB id: 4p5o

Contents

Protein chains

327 a.a.

75 a.a.

197 a.a.

169 a.a.

76 a.a.

Metals

_ZN ×6

PDB id:

4p5o

Name:

Ligase

Title:

Structure of an rbx1-ubc12~nedd8-cul1-dcn1 complex: a ring-e3- e2~ubiquitin-like protein-substrate intermediate trapped in action

Structure:

Cullin-1. Chain: a, c. Synonym: cul-1. Engineered: yes. Mutation: yes. E3 ubiquitin-protein ligase rbx1. Chain: b, d. Synonym: protein zyp,ring finger protein 75,ring-box protein 1,rbx1, regulator of cullins 1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cul1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rbx1, rnf75, roc1. Gene: dcun1d1, dcun1l1, rp42, sccro. Gene: ube2m, ubc12.

Resolution:

3.11Å R-factor: 0.230 R-free: 0.284

Authors:

D.C.Scott,B.A.Schulman

Key ref:

D.C.Scott et al. (2014). Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8. Cell, 157, 1671-1684. PubMed id: 24949976 DOI: 10.1016/j.cell.2014.04.037

Date:

18-Mar-14 Release date: 02-Jul-14

Protein chains

Q13616  (CUL1_HUMAN) -  Cullin-1 from Homo sapiens

Seq: 776 a.a.

Struc: 327 a.a.*

Protein chains

P62877  (RBX1_HUMAN) -  E3 ubiquitin-protein ligase RBX1 from Homo sapiens

Seq: 108 a.a.

Struc: 75 a.a.

Protein chains

Q96GG9  (DCNL1_HUMAN) -  DCN1-like protein 1 from Homo sapiens

Seq: 259 a.a.

Struc: 197 a.a.

Protein chains

P61081  (UBC12_HUMAN) -  NEDD8-conjugating enzyme Ubc12 from Homo sapiens

Seq: 183 a.a.

Struc: 169 a.a.*

Protein chains

Q15843  (NEDD8_HUMAN) -  NEDD8 from Homo sapiens

Seq: 81 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, E, K, C, F, H: E.C.?
• Enzyme class 3: Chains B, D: 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 4: Chains B, D: E.C.2.3.2.32 - cullin-RING-type E3 NEDD8 transferase.
• Reaction: S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]- L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N₆-[NEDD8- protein]-yl-[cullin]-L-lysine
• Enzyme class 5: Chains I, G: E.C.2.3.2.34 - E2 NEDD8-conjugating enzyme.
• Reaction: [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine + [E2 NEDD8- conjugating enzyme]-L-cysteine = [E1 NEDD8-activating enzyme]-L-cysteine + [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-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.

DOI no: 10.1016/j.cell.2014.04.037

Cell 157:1671-1684 (2014)

PubMed id: 24949976

Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8.

D.C.Scott, V.O.Sviderskiy, J.K.Monda, J.R.Lydeard, S.E.Cho, J.W.Harper, B.A.Schulman.

ABSTRACT

Most E3 ligases use a RING domain to activate a thioester-linked E2∼ubiquitin-like protein (UBL) intermediate and promote UBL transfer to a remotely bound target protein. Nonetheless, RING E3 mechanisms matching a specific UBL and acceptor lysine remain elusive, including for RBX1, which mediates NEDD8 ligation to cullins and >10% of all ubiquitination. We report the structure of a trapped RING E3-E2∼UBL-target intermediate representing RBX1-UBC12∼NEDD8-CUL1-DCN1, which reveals the mechanism of NEDD8 ligation and how a particular UBL and acceptor lysine are matched by a multifunctional RING E3. Numerous mechanisms specify cullin neddylation while preventing noncognate ubiquitin ligation. Notably, E2-E3-target and RING-E2∼UBL modules are not optimized to function independently, but instead require integration by the UBL and target for maximal reactivity. The UBL and target regulate the catalytic machinery by positioning the RING-E2∼UBL catalytic center, licensing the acceptor lysine, and influencing E2 reactivity, thereby driving their specific coupling by a multifunctional RING E3.