PDBsum entry 4mdk

Ligase/ligase inhibitor

PDB id: 4mdk

Contents

Protein chains

168 a.a.

157 a.a.

76 a.a.

Ligands

U94 ×4

Waters ×46

PDB id:

4mdk

Name:

Ligase/ligase inhibitor

Title:

Cdc34-ubiquitin-cc0651 complex

Structure:

Ubiquitin-conjugating enzyme e2 r1. Chain: a, b, c, d. Fragment: e2 domain (unp residues 7-184). Synonym: ubiquitin-conjugating enzyme e2-32 kda complementing, ubiquitin-conjugating enzyme e2-cdc34, ubiquitin-protein ligase r1. Engineered: yes. Ubiquitin. Chain: e, f, g, h. Fragment: unp residues 76-152.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdc34, ubch3, ube2r1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: ubc.

Resolution:

2.61Å R-factor: 0.207 R-free: 0.259

Authors:

D.F.Ceccarelli,S.Orlicky,M.Tyers,F.Sicheri

Key ref:

H.Huang et al. (2014). E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin. Nat Chem Biol, 10, 156-163. PubMed id: 24316736 DOI: 10.1038/nchembio.1412

Date:

22-Aug-13 Release date: 11-Dec-13

Protein chains

P49427  (UB2R1_HUMAN) -  Ubiquitin-conjugating enzyme E2 R1 from Homo sapiens

Seq: 236 a.a.

Struc: 168 a.a.

Protein chain

P49427  (UB2R1_HUMAN) -  Ubiquitin-conjugating enzyme E2 R1 from Homo sapiens

Seq: 236 a.a.

Struc: 157 a.a.

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: 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 3: Chains A, B, C, D: 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 4: Chains E, F, G, H: 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: 10.1038/nchembio.1412

Nat Chem Biol 10:156-163 (2014)

PubMed id: 24316736

E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.

H.Huang, D.F.Ceccarelli, S.Orlicky, D.J.St-Cyr, A.Ziemba, P.Garg, S.Plamondon, M.Auer, S.Sidhu, A.Marinier, G.Kleiger, M.Tyers, F.Sicheri.

ABSTRACT

Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.