4Y8I

Yeast 20S proteasome in complex with Ac-PLL-ep

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors.

Huber, E.M., de Bruin, G., Heinemeyer, W., Paniagua Soriano, G., Overkleeft, H.S., Groll, M.

(2015) J Am Chem Soc 137: 7835-7842

  • DOI: 10.1021/jacs.5b03688
  • Primary Citation of Related Structures:  
    4Y69, 4Y6A, 4Y6V, 4Y6Z, 4Y70, 4Y74, 4Y75, 4Y77, 4Y78, 4Y7W, 4Y7X, 4Y7Y, 4Y80, 4Y81, 4Y82, 4Y84, 4Y8G, 4Y8H, 4Y8I, 4Y8J, 4Y8K, 4Y8L, 4Y8M, 4Y8N, 4Y8O, 4Y8P, 4Y8Q, 4Y8R, 4Y8S, 4Y8T, 4Y8U, 4Y9Y, 4Y9Z, 4YA0, 4YA1, 4YA2, 4YA3, 4YA4, 4YA5, 4YA7, 4YA9

  • PubMed 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 ...

    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 α',β'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 β2c selective compound Ac-LAE-ep represents a promising starting point for the development of compounds that discriminate between β2c and β2i. (3) The compound Ac-LAA-ep was found to favor subunit β5c over β5i by three orders of magnitude. (4) Yeast β1 and human β1c 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 β1/2 substrate binding channel give rise to the β1 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.

    Organizational Affiliation: 

    †Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, 85748 Garching, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3B, P258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, Q254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6E, S234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7F, T288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1G, U252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
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Entity ID: 8
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Proteasome subunit beta type-2H, V232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1, YOR157C
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3, YER094C
EC: 3.4.25.1
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1, YER012W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K, Y212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2, DOA3, PRG1, YPR103W, P8283.10
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6L, Z222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7, PRS3, PTS1, YBL041W, YBL0407
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7M,
AA [auth a]		246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4, YFR050C
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1N,
BA [auth b]		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3, YJL001W, J1407
EC: 3.4.25.1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Ac-PLL-ep5synthetic constructMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
NA [auth K],
SA [auth Y]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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JA [auth G],
QA [auth N],
RA [auth U],
UA [auth b]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
IA [auth G],
KA [auth I],
LA [auth I],
MA [auth K],
OA [auth L],
IA [auth G],
KA [auth I],
LA [auth I],
MA [auth K],
OA [auth L],
PA [auth N],
TA [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.82α = 90
b = 298.32β = 113.06
c = 145.62γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-16 
  • Released Date: 2015-06-17 
    • Deposition Author(s): Huber, E.M., Groll, M.
Funding OrganizationLocationGrant Number
DFGGermanyGR1861/10-1
DFGGermanySFB1035/A2

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references