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PDBsum entry 2zcy

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2zcy
Jmol
Contents
Protein chains
250 a.a. *
244 a.a. *
241 a.a. *
242 a.a. *
233 a.a. *
244 a.a. *
243 a.a. *
222 a.a. *
204 a.a. *
198 a.a. *
212 a.a. *
222 a.a. *
233 a.a. *
196 a.a. *
Ligands
SRG ×6
Waters ×1018
* Residue conservation analysis
PDB id:
2zcy
Name: Hydrolase
Title: Yeast 20s proteasome:syringolin a-complex
Structure: Proteasome component y7. Chain: a, o. Synonym: macropain subunit y7, proteinase ysce subunit 7, multicatalytic endopeptidase complex subunit y7. Proteasome component y13. Chain: b, p. Synonym: macropain subunit y13, proteinase ysce subunit 13, multicatalytic endopeptidase complex subunit y13. Proteasome component pre6.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: w303. Strain: w303
Resolution:
2.90Å     R-factor:   0.215     R-free:   0.245
Authors: M.Groll,R.Dudler,M.Kaiser
Key ref:
M.Groll et al. (2008). A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism. Nature, 452, 755-758. PubMed id: 18401409 DOI: 10.1038/nature06782
Date:
15-Nov-07     Release date:   08-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2
Seq:
Struc:
250 a.a.
250 a.a.
Protein chains
Pfam   ArchSchema ?
P23638  (PSA4_YEAST) -  Proteasome subunit alpha type-3
Seq:
Struc:
258 a.a.
244 a.a.
Protein chains
Pfam   ArchSchema ?
P40303  (PSA7_YEAST) -  Proteasome subunit alpha type-4
Seq:
Struc:
254 a.a.
241 a.a.
Protein chains
Pfam   ArchSchema ?
P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5
Seq:
Struc:
260 a.a.
242 a.a.
Protein chains
Pfam   ArchSchema ?
P40302  (PSA1_YEAST) -  Proteasome subunit alpha type-6
Seq:
Struc:
234 a.a.
233 a.a.
Protein chains
Pfam   ArchSchema ?
P21242  (PSA3_YEAST) -  Probable proteasome subunit alpha type-7
Seq:
Struc:
288 a.a.
244 a.a.
Protein chains
Pfam   ArchSchema ?
P21243  (PSA6_YEAST) -  Proteasome subunit alpha type-1
Seq:
Struc:
252 a.a.
243 a.a.
Protein chains
Pfam   ArchSchema ?
P25043  (PSB7_YEAST) -  Proteasome subunit beta type-2
Seq:
Struc:
261 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3
Seq:
Struc:
205 a.a.
204 a.a.
Protein chains
Pfam   ArchSchema ?
P22141  (PSB2_YEAST) -  Proteasome subunit beta type-4
Seq:
Struc:
198 a.a.
198 a.a.
Protein chains
Pfam   ArchSchema ?
P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5
Seq:
Struc:
287 a.a.
212 a.a.
Protein chains
Pfam   ArchSchema ?
P23724  (PSB1_YEAST) -  Proteasome subunit beta type-6
Seq:
Struc:
241 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P30657  (PSB4_YEAST) -  Proteasome subunit beta type-7
Seq:
Struc:
266 a.a.
233 a.a.
Protein chains
Pfam   ArchSchema ?
P38624  (PSB6_YEAST) -  Proteasome subunit beta type-1
Seq:
Struc:
215 a.a.
196 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1: E.C.3.4.25.1  - Proteasome endopeptidase complex.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage at peptide bonds with very broad specificity.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nuclear outer membrane-endoplasmic reticulum membrane network   10 terms 
  Biological process     proteolysis   8 terms 
  Biochemical function     molecular_function     8 terms  

 

 
DOI no: 10.1038/nature06782 Nature 452:755-758 (2008)
PubMed id: 18401409  
 
 
A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism.
M.Groll, B.Schellenberg, A.S.Bachmann, C.R.Archer, R.Huber, T.K.Powell, S.Lindow, M.Kaiser, R.Dudler.
 
  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. 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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Syringolin-negative mutant exhibits reduced virulence. Five pots per experiment (Exp), each with eight 18-day-old bean plants, were spray-inoculated with 10^5 cells per millilitre of wild-type or SylA-negative (sylC KO) strains of Pss B728a. Lesion numbers per trifoliate leaf were counted on the oldest (O) and middle-aged (M) leaves. Mean lesion numbers s.d. over the five replica pots are given. p, error probability (two-sided t-test).
Figure 3.
Figure 3: Structural basis for proteasome inhibition by syrbactins. a, Chemical structure of SylA and GlbA. Red, , -unsaturated carbonyl group reacting with Thr1O^ ; green, dipeptide bond stabilizing the inhibitor upon proteasome binding; blue, molecule part determining active site specificity; yellow, aliphatic tail of GlbA. b, Mechanism of binding of SylA/GlbA to the active site Thr1. c, d, Stereo representation of the chymotryptic-like active site (rose, subunit 5; light blue, subunit 6) in complex with (c) SylA (green; PDB accession code ) and (d) GlbA (green, aliphatic tail in yellow; PDB accession code ). Magenta, covalent linkage of inhibitors with active site Thr1; dotted lines indicate hydrogen bonds. Black, residues performing specific interactions with SylA and GlbA. Electron-density maps (grey) are contoured from 1 in similar orientations around Thr1. e, Electrostatic potential surface (contoured from +15kT/e (intense blue) to -15kT/e (intense red)) of SylA bound to subunit 5. f, Structural superposition of SylA (green) with GlbA (yellow) bound to subunit 5.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 452, 755-758) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227738 A.Block, and J.R.Alfano (2011).
Plant targets for Pseudomonas syringae type III effectors: virulence targets or guarded decoys?
  Curr Opin Microbiol, 14, 39-46.  
20830349 J.Clerc, N.Li, D.Krahn, M.Groll, A.S.Bachmann, B.I.Florea, H.S.Overkleeft, and M.Kaiser (2011).
The natural product hybrid of Syringolin A and Glidobactin A synergizes proteasome inhibition potency with subsite selectivity.
  Chem Commun (Camb), 47, 385-387.  
21226105 S.Osman, B.J.Albert, Y.Wang, M.Li, N.L.Czaicki, and K.Koide (2011).
Structural requirements for the antiproliferative activity of pre-mRNA splicing inhibitor FR901464.
  Chemistry, 17, 895-904.  
20814885 A.Baldisserotto, C.Franceschini, F.Scalambra, C.Trapella, M.Marastoni, F.Sforza, R.Gavioli, and R.Tomatis (2010).
Synthesis and proteasome inhibition of N-allyl vinyl ester-based peptides.
  J Pept Sci, 16, 659-663.  
21203527 A.J.Dowling, P.A.Wilkinson, M.T.Holden, M.A.Quail, S.D.Bentley, J.Reger, N.R.Waterfield, R.W.Titball, and R.H.Ffrench-Constant (2010).
Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243.
  PLoS One, 5, e15693.  
20042019 C.Gu, I.Kolodziejek, J.Misas-Villamil, T.Shindo, T.Colby, M.Verdoes, K.H.Richau, J.Schmidt, H.S.Overkleeft, and R.A.van der Hoorn (2010).
Proteasome activity profiling: a simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities.
  Plant J, 62, 160-170.  
21035730 H.J.Imker, D.Krahn, J.Clerc, M.Kaiser, and C.T.Walsh (2010).
N-acylation during glidobactin biosynthesis by the tridomain nonribosomal peptide synthetase module GlbF.
  Chem Biol, 17, 1077-1083.  
20422068 J.J.La Clair (2010).
Natural product mode of action (MOA) studies: a link between natural and synthetic worlds.
  Nat Prod Rep, 27, 969-995.  
20030592 W.Wilk, T.J.Zimmermann, M.Kaiser, and H.Waldmann (2010).
Principles, implementation, and application of biology-oriented synthesis (BIOS).
  Biol Chem, 391, 491-497.  
19863801 C.Ramel, M.Tobler, M.Meyer, L.Bigler, M.O.Ebert, B.Schellenberg, and R.Dudler (2009).
Biosynthesis of the proteasome inhibitor syringolin A: the ureido group joining two amino acids originates from bicarbonate.
  BMC Biochem, 10, 26.  
19844639 H.Gross, and J.E.Loper (2009).
Genomics of secondary metabolite production by Pseudomonas spp.
  Nat Prod Rep, 26, 1408-1446.  
19968303 H.J.Imker, C.T.Walsh, and W.M.Wuest (2009).
SylC catalyzes ureido-bond formation during biosynthesis of the proteasome inhibitor syringolin A.
  J Am Chem Soc, 131, 18263-18265.  
19746508 J.Clerc, B.I.Florea, M.Kraus, M.Groll, R.Huber, A.S.Bachmann, R.Dudler, C.Driessen, H.S.Overkleeft, and M.Kaiser (2009).
Syringolin A selectively labels the 20 S proteasome in murine EL4 and wild-type and bortezomib-adapted leukaemic cell lines.
  Chembiochem, 10, 2638-2643.  
19359491 J.Clerc, M.Groll, D.J.Illich, A.S.Bachmann, R.Huber, B.Schellenberg, R.Dudler, and M.Kaiser (2009).
Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition.
  Proc Natl Acad Sci U S A, 106, 6507-6512.
PDB code: 3gpj
19540926 J.D.Lewis, D.S.Guttman, and D.Desveaux (2009).
The targeting of plant cellular systems by injected type III effector proteins.
  Semin Cell Dev Biol, 20, 1055-1063.  
19109822 M.Groll, R.Huber, and L.Moroder (2009).
The persisting challenge of selective and specific proteasome inhibition.
  J Pept Sci, 15, 58-66.  
19624732 S.Sollner, and P.Macheroux (2009).
New roles of flavoproteins in molecular cell biology: an unexpected role for quinone reductases as regulators of proteasomal degradation.
  FEBS J, 276, 4313-4324.  
19400727 T.Boller, and G.Felix (2009).
A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors.
  Annu Rev Plant Biol, 60, 379-406.  
19523153 T.Spallek, S.Robatzek, and V.Göhre (2009).
How microbes utilize host ubiquitination.
  Cell Microbiol, 11, 1425-1434.  
18771922 M.Trujillo, K.Ichimura, C.Casais, and K.Shirasu (2008).
Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.
  Curr Biol, 18, 1396-1401.  
19062288 V.Göhre, T.Spallek, H.Häweker, S.Mersmann, T.Mentzel, T.Boller, M.de Torres, J.W.Mansfield, and S.Robatzek (2008).
Plant pattern-recognition receptor FLS2 is directed for degradation by the bacterial ubiquitin ligase AvrPtoB.
  Curr Biol, 18, 1824-1832.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.