PDBsum entry 8v0d

Ligase

PDB id: 8v0d

Contents

Protein chains

213 a.a.

Metals

_ZN ×5

Waters ×39

PDB id:

8v0d

Name:

Ligase

Title:

Ubch5b-ring3 of mib1 fusion structure

Structure:

Ubch5b-ring3 of mib1 fusion protein. Chain: b, a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d2, pubc1, ubc4, ubc5b, ubch4, ubch5b, mib1, dip1, kiaa1323, zzank2. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.40Å R-factor: 0.214 R-free: 0.243

Authors:

R.Cao,S.C.Blacklow

Key ref:

R.Cao and s.c.blacklow Ubch5b-Ring3 fusion structure. To be published, . PubMed id: 39121852

Date:

17-Nov-23 Release date: 27-Nov-24

Protein chains

P62837  (UB2D2_HUMAN) -  Ubiquitin-conjugating enzyme E2 D2 from Homo sapiens

Seq: 147 a.a.

Struc: 213 a.a.

Protein chains

Q86YT6  (MIB1_HUMAN) -  E3 ubiquitin-protein ligase MIB1 from Homo sapiens

Seq: 1006 a.a.

Struc: 213 a.a.*

* PDB and UniProt seqs differ at 143 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: 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 2: E.C.2.3.2.24 - (E3-independent) E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N₆- monoubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 3: 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

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.