4LTC image
Deposition Date 2013-07-23
Release Date 2014-07-02
Last Version Date 2024-10-09
Entry Detail
PDB ID:
4LTC
Title:
Crystal structure of yeast 20S proteasome in complex with enone carmaphycin analogue 6
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-2
Gene (Uniprot):PRE8
Chain IDs:A, H (auth: O)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-3
Gene (Uniprot):PRE9
Chain IDs:B, I (auth: P)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-4
Gene (Uniprot):PRE6
Chain IDs:C, J (auth: Q)
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-5
Gene (Uniprot):PUP2
Chain IDs:D, K (auth: R)
Chain Length:260
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-6
Gene (Uniprot):PRE5
Chain IDs:E, L (auth: S)
Chain Length:234
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Probable proteasome subunit alpha type-7
Gene (Uniprot):PRE10
Chain IDs:F, M (auth: T)
Chain Length:287
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-1
Gene (Uniprot):SCL1
Chain IDs:G, N (auth: U)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-2
Gene (Uniprot):PUP1
Chain IDs:O (auth: H), V
Chain Length:232
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-3
Gene (Uniprot):PUP3
Chain IDs:P (auth: I), W
Chain Length:205
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-4
Gene (Uniprot):PRE1
Chain IDs:Q (auth: J), X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-5
Gene (Uniprot):PRE2
Chain IDs:R (auth: K), Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-6
Gene (Uniprot):PRE7
Chain IDs:S (auth: L), Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-7
Gene (Uniprot):PRE4
Chain IDs:T (auth: M), AA (auth: a)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-1
Gene (Uniprot):PRE3
Chain IDs:U (auth: N), BA (auth: b)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Peptide-like Molecules
PRD_001161
Primary Citation
Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor.
Chem.Biol. 21 782 791 (2014)
PMID: 24930969 DOI: 10.1016/j.chembiol.2014.04.010

Abstact

Hydroamination reactions involving the addition of an amine to an inactivated alkene are entropically prohibited and require strong chemical catalysts. While this synthetic process is efficient at generating substituted amines, there is no equivalent in small molecule-mediated enzyme inhibition. We report an unusual mechanism of proteasome inhibition that involves a hydroamination reaction of alkene derivatives of the epoxyketone natural product carmaphycin. We show that the carmaphycin enone first forms a hemiketal intermediate with the catalytic Thr1 residue of the proteasome before cyclization by an unanticipated intramolecular alkene hydroamination reaction, resulting in a stable six-membered morpholine ring. The carmaphycin enone electrophile, which does not undergo a 1,4-Michael addition as previously observed with vinyl sulfone and α,β-unsaturated amide-based inhibitors, is partially reversible and gives insight into the design of proteasome inhibitors for cancer chemotherapy.

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