3MG6: Structure of yeast 20S open-gate proteasome with Compound 6

Citation:
Abstract
The mammalian 26S proteasome is a 2500 kDa multi-catalytic complex involved in intracellular protein degradation. We describe the synthesis and properties of a novel series of non-covalent di-peptide inhibitors of the proteasome based [corrected] on a capped tri-peptide that was first identified by high-throughput screening of a library of approx. 350000 compounds for inhibitors of the ubiquitin-proteasome system in cells. We show that these compounds are entirely selective for the beta5 (chymotrypsin-like) site over the beta1 (caspase-like) and beta2 (trypsin-like) sites of the 20S core particle of the proteasome, and over a panel of less closely related proteases. Compound optimization, guided by X-ray crystallography of the liganded 20S core particle, confirmed their non-covalent binding mode and provided a structural basis for their enhanced in vitro and cellular potencies. We demonstrate that such compounds show low nanomolar IC50 values for the human 20S beta5 site in vitro, and that pharmacological inhibition of this site in cells is sufficient to potently inhibit the degradation of a tetra-ubiquitin-luciferase reporter, activation of NFkappaB (nuclear factor kappaB) in response to TNF-alpha (tumour necrosis factor-alpha) and the proliferation of cancer cells. Finally, we identified capped di-peptides that show differential selectivity for the beta5 site of the constitutively expressed proteasome and immunoproteasome in vitro and in B-cell lymphomas. Collectively, these studies describe the synthesis, activity and binding mode of a new series of non-covalent proteasome inhibitors with unprecedented potency and selectivity for the beta5 site, and which can discriminate between the constitutive proteasome and immunoproteasome in vitro and in cells.
PDB ID: 3MG6Download
MMDB ID: 90594
PDB Deposition Date: 2010/4/5
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Similar Structures:
Biological Unit for 3MG6: 28-meric; determined by author and by software (PISA)
Molecular Components in 3MG6
Label Count Molecule
Proteins (28 molecules)
2
Proteasome Component Y7(Gene symbol: PRE8)
Molecule annotation
2
Proteasome Component Y13(Gene symbol: PRE9)
Molecule annotation
2
Proteasome Component Pre6(Gene symbol: PRE6)
Molecule annotation
2
Proteasome Component Pup2(Gene symbol: PUP2)
Molecule annotation
2
Proteasome Component Pre5(Gene symbol: PRE5)
Molecule annotation
2
Proteasome Component C1(Gene symbol: PRE10)
Molecule annotation
2
Proteasome Component C7-alpha(Gene symbol: SCL1)
Molecule annotation
2
Proteasome Component Pup1(Gene symbol: PUP1)
Molecule annotation
2
Proteasome Component Pup3(Gene symbol: PUP3)
Molecule annotation
2
Proteasome Component C11(Gene symbol: PRE1)
Molecule annotation
2
Proteasome Component Pre2(Gene symbol: PRE2)
Molecule annotation
2
Proteasome Component C5(Gene symbol: PRE7)
Molecule annotation
2
Proteasome Component Pre4(Gene symbol: PRE4)
Molecule annotation
2
Proteasome Component Pre3(Gene symbol: PRE3)
Molecule annotation
Chemicals (14 molecules)
1
10
2
2
3
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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