PDBsum entry 3gpj

Hydrolase

PDB id: 3gpj

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

SY2 ×4

Waters ×1335

* Residue conservation analysis

PDB id:

3gpj

Name:

Hydrolase

Title:

Crystal structure of the yeast 20s proteasome in complex with syringolin b

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. Fragment: sequence database residues 2-245. Synonym: macropain subunit y13, proteinase ysce subunit 13, multicatalytic endopeptidase complex subunit y13.

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Organism_taxid: 4932

Resolution:

2.70Å R-factor: 0.250 R-free: 0.264

Authors:

M.Groll,R.Huber,M.Kaiser

Key ref:

J.Clerc et al. (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. PubMed id: 19359491 DOI: 10.1073/pnas.0901982106

Date:

23-Mar-09 Release date: 02-Jun-09

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, 1, 2: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.

DOI no: 10.1073/pnas.0901982106

Proc Natl Acad Sci U S A 106:6507-6512 (2009)

PubMed id: 19359491

Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition.

J.Clerc, M.Groll, D.J.Illich, A.S.Bachmann, R.Huber, B.Schellenberg, R.Dudler, M.Kaiser.

ABSTRACT

Syrbactins, a family of natural products belonging either to the syringolin or glidobactin class, are highly potent proteasome inhibitors. Although sharing similar structural features, they differ in their macrocyclic lactam core structure and exocyclic side chain. These structural variations critically influence inhibitory potency and proteasome subsite selectivity. Here, we describe the total synthesis of syringolin A and B, which together with enzyme kinetic and structural studies, allowed us to elucidate the structural determinants underlying the proteasomal subsite selectivity and binding affinity of syrbactins. These findings were used successfully in the rational design and synthesis of a syringolin A-based lipophilic derivative, which proved to be the most potent syrbactin-based proteasome inhibitor described so far. With a K(i)' of 8.65 +/- 1.13 nM for the chymotryptic activity, this syringolin A derivative displays a 100-fold higher potency than the parent compound syringolin A. In light of the medicinal relevance of proteasome inhibitors as anticancer compounds, the present findings may assist in the rational design and development of syrbactin-based chemotherapeutics.

Selected figure(s)

Figure 1.
Structures of SylA (1), SylB (2), GlbA (3), and the lipophilic SylA derivative 21.

Figure 4.
X-ray analysis of the complex of SylB (2) and the 20S proteasome and comparison with other syrbactins. (A) Structure of syringolin A (1) and B (2). (B) Electrostatic potential surface [contoured from +15 kT/e (intense blue) to −15 kT/e (intense red)] of SylB covalently bound to β5. (C) Stereo representation of SylB (2) bound to the chymotryptic like active site in complex with 20S proteasome (rose, subunit β5; gray, subunit β6). (D) Structural superimposition of SylA (1, yellow), SylB (2, green), and GlbA (3, light gray).

Figures were selected by an automated process.