PDBsum entry 2zcy

Hydrolase

PDB id: 2zcy

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

Protein chains

P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 250 a.a.

Struc: 250 a.a.

Protein chains

P23638  (PSA3_YEAST) -  Proteasome subunit alpha type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 258 a.a.

Struc: 244 a.a.

Protein chains

P40303  (PSA4_YEAST) -  Proteasome subunit alpha type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 241 a.a.

Protein chains

P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 260 a.a.

Struc: 242 a.a.

Protein chains

P40302  (PSA6_YEAST) -  Proteasome subunit alpha type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 234 a.a.

Struc: 233 a.a.

Protein chains

P21242  (PSA7_YEAST) -  Probable proteasome subunit alpha type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 288 a.a.

Struc: 244 a.a.

Protein chains

P21243  (PSA1_YEAST) -  Proteasome subunit alpha type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 243 a.a.

Protein chains

P25043  (PSB2_YEAST) -  Proteasome subunit beta type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 222 a.a.

Protein chains

P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 205 a.a.

Struc: 204 a.a.

Protein chains

P22141  (PSB4_YEAST) -  Proteasome subunit beta type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 198 a.a.

Struc: 198 a.a.

Protein chains

P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 287 a.a.

Struc: 212 a.a.

Protein chains

P23724  (PSB6_YEAST) -  Proteasome subunit beta type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 241 a.a.

Struc: 222 a.a.

Protein chains

P30657  (PSB7_YEAST) -  Proteasome subunit beta type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 266 a.a.

Struc: 233 a.a.

Protein chains

P38624  (PSB1_YEAST) -  Proteasome subunit beta type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 196 a.a.

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.
• Reaction: Cleavage at peptide bonds with very broad specificity.

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.