4HRD image
Deposition Date 2012-10-27
Release Date 2014-01-29
Last Version Date 2024-10-16
Entry Detail
PDB ID:
4HRD
Title:
Crystal structure of yeast 20S proteasome in complex with the natural product carmaphycin A
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.80 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 component Y7
Gene (Uniprot):PRE8
Chain IDs:A, O
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component Y13
Gene (Uniprot):PRE9
Chain IDs:B, P
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE6
Gene (Uniprot):PRE6
Chain IDs:C, Q
Chain Length:241
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP2
Gene (Uniprot):PUP2
Chain IDs:D, R
Chain Length:242
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE5
Gene (Uniprot):PRE5
Chain IDs:E, S
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C1
Gene (Uniprot):PRE10
Chain IDs:F, T
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C7-alpha
Gene (Uniprot):SCL1
Chain IDs:G, U
Chain Length:243
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP1
Gene (Uniprot):PUP1
Chain IDs:H, V
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PUP3
Gene (Uniprot):PUP3
Chain IDs:I, W
Chain Length:204
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C11
Gene (Uniprot):PRE1
Chain IDs:J, X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE2
Gene (Uniprot):PRE2
Chain IDs:K, Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component C5
Gene (Uniprot):PRE7
Chain IDs:L, Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE4
Gene (Uniprot):PRE4
Chain IDs:M, AA (auth: a)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Proteasome component PRE3
Gene (Uniprot):PRE3
Chain IDs:N, BA (auth: b)
Chain Length:244
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Ligand Molecules
Peptide-like Molecules
PRD_000956
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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