3DY3

Crystal structure of yeast 20S proteasome in complex with the epimer form of spirolactacystin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analysis of spiro beta-lactone proteasome inhibitors.

Groll, M.Balskus, E.P.Jacobsen, E.N.

(2008) J.Am.Chem.Soc. 130: 14981-14983

  • DOI: 10.1021/ja806059t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Spiro beta-lactone-based proteasome inhibitors were discovered in the context of an asymmetric catalytic total synthesis of the natural product (+)-lactacystin (1). Lactone 4 was found to be a potent inhibitor of the 26S proteasome, while its C-6 epi ...

    Spiro beta-lactone-based proteasome inhibitors were discovered in the context of an asymmetric catalytic total synthesis of the natural product (+)-lactacystin (1). Lactone 4 was found to be a potent inhibitor of the 26S proteasome, while its C-6 epimer (5) displayed weak activity. Crystallographic studies of the two analogues covalently bound to the 20S proteasome permitted characterization of the important stabilizing interactions between each inhibitor and the proteasome's key catalytic N-terminal threonine residue. This structural data support the hypothesis that the discrepancy in potency between 4 and 5 may be due to differences in the hydrolytic stabilities of the resulting acyl enzyme complexes.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y7
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y13
B, P
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE6
C, Q
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP2
D, R
242Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE5
E, S
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C1
F, T
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C7-alpha
G, U
243Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP1
H, V
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP3
I, W
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C11
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE2
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C5
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE4
M, 1
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE3
N, 2
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLR
Query on SLR

Download SDF File 
Download CCD File 
K, Y
(3R,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxo-D-proline
C10 H17 N O5
USVJHCXEVSVUEZ-JTGULSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 135.148α = 90.00
b = 301.860β = 112.81
c = 144.084γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
CNSphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance