PDBsum entry 5ulh

Transferase

PDB id: 5ulh

Contents

Protein chains

148 a.a.

75 a.a.

51 a.a.

Ligands

GOL ×2

SCN ×2

Metals

_ZN ×2

Waters ×68

PDB id:

5ulh

Name:

Transferase

Title:

Structure of rnf165 in complex with a ubch5b~ub conjugate

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a. Synonym: (e3-independent) e2 ubiquitin-conjugating enzyme d2,e2 ubiquitin-conjugating enzyme d2,ubiquitin carrier protein d2, ubiquitin-conjugating enzyme e2(17)kb 2,ubiquitin-conjugating enzyme e2-17 kda 2,ubiquitin-protein ligase d2,p53-regulated ubiquitin- conjugating enzyme 1. Engineered: yes. Mutation: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d2, pubc1, ubc4, ubc5b, ubch4, ubch5b. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_cell_line: bl21. Gene: ubb. Gene: rnf165.

Resolution:

1.95Å R-factor: 0.190 R-free: 0.217

Authors:

A.J.Middleton,C.L.Day,J.D.Wright

Key ref:

A.J.Middleton et al. Discovery of new non-Covalent ubiquitin binding sites ubch5. To be published, .

Date:

24-Jan-17 Release date: 07-Jun-17

Protein chain

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

Seq: 147 a.a.

Struc: 148 a.a.*

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 75 a.a.

Protein chain

Q6ZSG1  (RN165_HUMAN) -  E3 ubiquitin-protein ligase ARK2C from Homo sapiens

Seq: 346 a.a.

Struc: 51 a.a.*

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

Enzyme reactions

• Enzyme class 1: Chain A: E.C.2.3.2.23 - 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: Chain A: 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: Chain B: E.C.?
• Enzyme class 4: Chain C: 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.