PDBsum entry 4lcd

Ligase/protein binding

PDB id: 4lcd

Contents

Protein chains

419 a.a.

14 a.a.

75 a.a.

Ligands

GLN-PRO-PRO-ALA-TYR-ASP-GLU-ASP

PDB id:

4lcd

Name:

Ligase/protein binding

Title:

Structure of an rsp5xubxsna3 complex: mechanism of ubiquitin ligation and lysine prioritization by a hect e3

Structure:

E3 ubiquitin-protein ligase rsp5. Chain: a, b. Fragment: ww3 + hect (unp residues 383-809). Synonym: reverses spt-phenotype protein 5. Engineered: yes. Mutation: yes. Protein sna3. Chain: c, d. Fragment: cytosolic fragment (unp residues 104-127).

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: mdp1, npi1, rsp5, sygp-orf41, yer125w. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens.

Resolution:

3.10Å R-factor: 0.253 R-free: 0.299

Authors:

H.B.Kamadurai,D.Miller,B.A.Schulman

Key ref:

H.B.Kamadurai et al. (2013). Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Elife, 2, e00828. PubMed id: 23936628 DOI: 10.7554/eLife.00828

Date:

21-Jun-13 Release date: 14-Aug-13

Protein chains

P39940  (RSP5_YEAST) -  E3 ubiquitin-protein ligase RSP5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 809 a.a.

Struc: 419 a.a.*

Protein chain

P14359  (SNA3_YEAST) -  Protein SNA3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 133 a.a.

Struc: 14 a.a.

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 75 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.3.2.26 - HECT-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 D, E, 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: 10.7554/eLife.00828

Elife 2:e00828 (2013)

PubMed id: 23936628

Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.

H.B.Kamadurai, Y.Qiu, A.Deng, J.S.Harrison, C.Macdonald, M.Actis, P.Rodrigues, D.J.Miller, J.Souphron, S.M.Lewis, I.Kurinov, N.Fujii, M.Hammel, R.Piper, B.Kuhlman, B.A.Schulman.

ABSTRACT

Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT domain orienting the E3∼ubiquitin thioester bond for ligation, and restricting the location of the substrate-binding domain to prioritize target lysines for ubiquitination. The data allow visualization of an E2-to-E3-to-substrate ubiquitin transfer cascade, and show how HECT-specific ubiquitin interactions driving multiple reactions are repurposed by a major E3 conformational change to promote ligation. DOI:http://dx.doi.org/10.7554/eLife.00828.001.