6ZP8 image
Deposition Date 2020-07-08
Release Date 2021-05-19
Last Version Date 2024-10-16
Entry Detail
PDB ID:
6ZP8
Keywords:
Title:
Yeast 20S proteasome in complex with glidobactin-like natural product HB335
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-2
Gene (Uniprot):PRE8
Chain IDs:A, O
Chain Length:246
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-3
Gene (Uniprot):PRE9
Chain IDs:B, P
Chain Length:258
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-4
Gene (Uniprot):PRE6
Chain IDs:C, Q
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-5
Gene (Uniprot):PUP2
Chain IDs:D, R
Chain Length:260
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-6
Gene (Uniprot):PRE5
Chain IDs:E, S
Chain Length:234
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Probable proteasome subunit alpha type-7
Gene (Uniprot):PRE10
Chain IDs:F, T
Chain Length:288
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit alpha type-1
Gene (Uniprot):SCL1
Chain IDs:G, U
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-2
Gene (Uniprot):PUP1
Chain IDs:H, V
Chain Length:232
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-3
Gene (Uniprot):PUP3
Chain IDs:I, W
Chain Length:205
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-4
Gene (Uniprot):PRE1
Chain IDs:J, X
Chain Length:198
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-5
Gene (Uniprot):PRE2
Chain IDs:K, Y
Chain Length:212
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-6
Gene (Uniprot):PRE7
Chain IDs:L, Z
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-7
Gene (Uniprot):PRE4
Chain IDs:M, AA (auth: a)
Chain Length:246
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Polymer Type:polypeptide(L)
Molecule:Proteasome subunit beta type-1
Gene (Uniprot):PRE3
Chain IDs:N, BA (auth: b)
Chain Length:258
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288C
Peptide-like Molecules
PRD_002578
Primary Citation
Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-like Proteasome Inhibitors from Photorhabdus laumondii.
Chembiochem 22 1582 1588 (2021)
PMID: 33452852 DOI: 10.1002/cbic.202100014

Abstact

The glidobactin-like natural products (GLNPs) glidobactin A and cepafungin I have been reported to be potent proteasome inhibitors and are regarded as promising candidates for anticancer drug development. Their biosynthetic gene cluster (BGC) plu1881-1877 is present in entomopathogenic Photorhabdus laumondii but silent under standard laboratory conditions. Here we show the largest subset of GLNPs, which are produced and identified after activation of the silent BGC in the native host and following heterologous expression of the BGC in Escherichia coli. Their chemical diversity results from a relaxed substrate specificity and flexible product release in the assembly line of GLNPs. Crystal structure analysis of the yeast proteasome in complex with new GLNPs suggests that the degree of unsaturation and the length of the aliphatic tail are critical for their bioactivity. The results in this study provide the basis to engineer the BGC for the generation of new GLNPs and to optimize these natural products resulting in potential drugs for cancer therapy.

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Primary Citation of related structures