3BDM

yeast 20S proteasome:glidobactin A-complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism

Groll, M.Schellenberg, B.Bachmann, A.S.Archer, C.R.Huber, R.Powell, T.K.Lindow, S.Kaiser, M.Dudler, R.

(2008) Nature 452: 755-758

  • DOI: 10.1038/nature06782
  • Primary Citation of Related Structures:  
    2ZCY, 3BDM

  • PubMed Abstract: 
  • Pathogenic bacteria often use effector molecules to increase virulence. In most cases, the mode of action of effectors remains unknown. Strains of Pseudomonas syringae pv. syringae (Pss) secrete syringolin A (SylA), a product of a mixed non-ribosomal peptide/polyketide synthetase, in planta ...

    Pathogenic bacteria often use effector molecules to increase virulence. In most cases, the mode of action of effectors remains unknown. Strains of Pseudomonas syringae pv. syringae (Pss) secrete syringolin A (SylA), a product of a mixed non-ribosomal peptide/polyketide synthetase, in planta. Here we identify SylA as a virulence factor because a SylA-negative mutant in Pss strain B728a obtained by gene disruption was markedly less virulent on its host, Phaseolus vulgaris (bean). We show that SylA irreversibly inhibits all three catalytic activities of eukaryotic proteasomes, thus adding proteasome inhibition to the repertoire of modes of action of virulence factors. The crystal structure of the yeast proteasome in complex with SylA revealed a novel mechanism of covalent binding to the catalytic subunits. Thus, SylA defines a new class of proteasome inhibitors that includes glidobactin A (GlbA), a structurally related compound from an unknown species of the order Burkholderiales, for which we demonstrate a similar proteasome inhibition mechanism. As proteasome inhibitors are a promising class of anti-tumour agents, the discovery of a novel family of inhibitory natural products, which we refer to as syrbactins, may also have implications for the development of anti-cancer drugs. Homologues of SylA and GlbA synthetase genes are found in some other pathogenic bacteria, including the human pathogen Burkholderia pseudomallei, the causative agent of melioidosis. It is thus possible that these bacteria are capable of producing proteasome inhibitors of the syrbactin class.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y7A, O250Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component Y13B, P258Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE6C, Q254Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP2D, R260Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE5E, S234Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C1F, T287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C7-alphaG, U252Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP1H, V232Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PUP3I, W205Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C11J, X198Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE2K, Y212Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component C5L, Z241Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE4AA [auth 0], M266Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome component PRE3BA [auth 1], N196Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDT
Query on GDT

Download Ideal Coordinates CCD File 
CA [auth H], DA [auth K], EA [auth V], FA [auth Y](2E,4E)-N-[(2S,3R)-3-hydroxy-1-[[(3Z,5S,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]amino]-1-ox obutan-2-yl]dodeca-2,4-dienamide
C27 H44 N4 O6
TYGJUQYJMIOZLZ-HXSKNMNHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.77α = 90
b = 302.79β = 112.24
c = 143.21γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance