PDBsum entry 5aie

Ligase

PDB id: 5aie

Contents

Protein chains

54 a.a.

150 a.a.

Metals

_ZN ×2

PDB id:

5aie

Name:

Ligase

Title:

Not4 ring domain in complex with ubc4

Structure:

General negative regulator of transcription subunit 4. Chain: a. Fragment: ring domain, residues 30-83. Synonym: not4, modulator of transcription 2. Engineered: yes. Ubiquitin-conjugating enzyme e2 4. Chain: b. Synonym: ubc4, ubiquitin carrier protein 4, ubiquitin-protein ligase 4.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: s288c. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.

Resolution:

2.80Å R-factor: 0.225 R-free: 0.271

Authors:

V.Bhaskar,J.Basquin,E.Conti

Key ref:

V.Bhaskar et al. (2015). Architecture of the ubiquitylation module of the yeast Ccr4-Not complex. Structure, 23, 921-928. PubMed id: 25914052 DOI: 10.1016/j.str.2015.03.011

Date:

12-Feb-15 Release date: 29-Apr-15

Protein chain

P34909  (NOT4_YEAST) -  General negative regulator of transcription subunit 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 587 a.a.

Struc: 54 a.a.*

Protein chain

P15731  (UBC4_YEAST) -  Ubiquitin-conjugating enzyme E2 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 148 a.a.

Struc: 150 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.

DOI no: 10.1016/j.str.2015.03.011

Structure 23:921-928 (2015)

PubMed id: 25914052

Architecture of the ubiquitylation module of the yeast Ccr4-Not complex.

V.Bhaskar, J.Basquin, E.Conti.

ABSTRACT

The Ccr4-Not complex regulates eukaryotic gene expression at multiple levels, including mRNA turnover, translational repression, and transcription. We have studied the ubiquitylation module of the yeast Ccr4-Not complex and addressed how E3 ligase binds cognate E2 and how it is tethered to the complex. The 2.8-Å resolution crystal structure of the N-terminal RING domain of Not4 in complex with Ubc4 shows the detailed interactions of this E3-E2 complex. The 3.6-Å resolution crystal structure of the C-terminal domain of the yeast Not4 in complex with the C-terminal domain of Not1 reveals how a largely extended region at the C-terminus of Not4 wraps around a HEAT-repeat region of Not1. This C-terminal region of Not4 is only partly conserved in metazoans, rationalizing its weaker Not1-binding properties. The structural and biochemical data show how Not1 can incorporate both the ubiquitylation module and the Not2-Not3/5 module concomitantly in the Ccr4-Not complex.