4Y80: Yeast 20s Proteasome In Complex With Ac-lai-ep

Citation:
Abstract
Cleavage analyses of 20S proteasomes with natural or synthetic substrates allowed to infer the substrate specificities of the active sites and paved the way for the rational design of high-affinity proteasome inhibitors. However, details of cleavage preferences remained enigmatic due to the lack of appropriate structural data. In a unique approach, we here systematically examined substrate specificities of yeast and human proteasomes using irreversibly acting alpha',beta'epoxyketone (ep) inhibitors. Biochemical and structural analyses provide unique insights into the substrate preferences of the distinct active sites and highlight differences between proteasome types that may be considered in future inhibitor design efforts. (1) For steric reasons, epoxyketones with Val or Ile at the P1 position are weak inhibitors of all active sites. (2) Identification of the beta2c selective compound Ac-LAE-ep represents a promising starting point for the development of compounds that discriminate between beta2c and beta2i. (3) The compound Ac-LAA-ep was found to favor subunit beta5c over beta5i by three orders of magnitude. (4) Yeast beta1 and human beta1c subunits preferentially bind Asp and Leu in their S1 pockets, while Glu and large hydrophobic residues are not accepted. (5) Exceptional structural features in the beta1/2 substrate binding channel give rise to the beta1 selectivity of compounds featuring Pro at the P3 site. Altogether, 23 different epoxyketone inhibitors, five proteasome mutants, and 43 crystal structures served to delineate a detailed picture of the substrate and ligand specificities of proteasomes and will further guide drug development efforts toward subunit-specific proteasome inhibitors for applications as diverse as cancer and autoimmune disorders.
PDB ID: 4Y80Download
MMDB ID: 130112
PDB Deposition Date: 2015/2/16
Updated in MMDB: 2015/07
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
Similar Structures:
Biological Unit for 4Y80: 34-meric; determined by author
Molecular Components in 4Y80
Label Count Molecule
Proteins (28 molecules)
2
Proteasome Subunit Alpha Type-2(Gene symbol: PRE8)
Molecule annotation
2
Proteasome Subunit Alpha Type-3(Gene symbol: PRE9)
Molecule annotation
2
Proteasome Subunit Alpha Type-4(Gene symbol: PRE6)
Molecule annotation
2
Proteasome Subunit Alpha Type-5(Gene symbol: PUP2)
Molecule annotation
2
Proteasome Subunit Alpha Type-6(Gene symbol: PRE5)
Molecule annotation
2
Probable Proteasome Subunit Alpha Type-7(Gene symbol: PRE10)
Molecule annotation
2
Proteasome Subunit Alpha Type-1(Gene symbol: SCL1)
Molecule annotation
2
Proteasome Subunit Beta Type-2(Gene symbol: PUP1)
Molecule annotation
2
Proteasome Subunit Beta Type-3(Gene symbol: PUP3)
Molecule annotation
2
Proteasome Subunit Beta Type-4(Gene symbol: PRE1)
Molecule annotation
2
Proteasome Subunit Beta Type-5(Gene symbol: PRE2)
Molecule annotation
2
Proteasome Subunit Beta Type-6(Gene symbol: PRE7)
Molecule annotation
2
Proteasome Subunit Beta Type-7(Gene symbol: PRE4)
Molecule annotation
2
Proteasome Subunit Beta Type-1(Gene symbol: PRE3)
Molecule annotation
Nucleotide(1 molecule)
6
Ac-lai-ep
Molecule annotation
Chemicals (14 molecules)
1
7
2
4
3
3
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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