PDBsum entry 9khs

Ligase

PDB id: 9khs

Contents

Protein chains

148 a.a.

77 a.a.

76 a.a.

76 a.a.

802 a.a.

PDB id:

9khs

Name:

Ligase

Title:

Cryo-em structure of ufd2/ubc4-ub in complex with k29-linked diub (monomeric conformation)

Structure:

Ubiquitin-conjugating enzyme e2 4. Chain: b. Synonym: e2 ubiquitin-conjugating enzyme 4,ubiquitin carrier protein 4,ubiquitin-protein ligase 4. Engineered: yes. Mutation: yes. Polyubiquitin-c. Chain: d. Engineered: yes.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Organism_taxid: 559292. Gene: ubc4, ybr082c, ybr0745. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.

Authors:

H.S.Ai,Z.B.Tong,L.Liu

Key ref:

Z.B.Tong et al. Structural basis for the ubiquitin e4 enzyme ufd2-Cat k48/k29 branched ubiquitin chains. To be published, . PubMed id: 40817136

Date:

11-Nov-24 Release date: 30-Jul-25

Protein chain

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

Seq: 148 a.a.

Struc: 148 a.a.*

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 77 a.a.*

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

Protein chain

P62979  (RS27A_HUMAN) -  Ubiquitin-ribosomal protein eS31 fusion protein from Homo sapiens

Seq: 156 a.a.

Struc: 76 a.a.

Protein chain

P54860  (UFD2_YEAST) -  E4 ubiquitin-protein ligase UFD2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 961 a.a.

Struc: 802 a.a.

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: 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 2: 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.