PDBsum entry 1fnt

Hydrolase/hydrolase activator

PDB id: 1fnt

Contents

Protein chains

238 a.a. *

247 a.a. *

241 a.a. *

239 a.a. *

244 a.a. *

233 a.a. *

240 a.a. *

196 a.a. *

222 a.a. *

204 a.a. *

198 a.a. *

212 a.a. *

222 a.a. *

233 a.a. *

(+ 8 more) 198 a.a. *

Metals

_MG ×14

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for the activation of 20s proteasomes by 11s regulators.

Authors

F.G.Whitby, E.I.Masters, L.Kramer, J.R.Knowlton, Y.Yao, C.C.Wang, C.P.Hill.

Ref.

Nature, 2000, 408, 115-120. [DOI no: 10.1038/35040607]

PubMed id

11081519

Abstract

Most of the non-lysosomal proteolysis that occurs in eukaryotic cells is performed by a nonspecific and abundant barrel-shaped complex called the 20S proteasome. Substrates access the active sites, which are sequestered in an internal chamber, by traversing a narrow opening (alpha-annulus) that is blocked in the unliganded 20S proteasome by amino-terminal sequences of alpha-subunits. Peptide products probably exit the 20S proteasome through the same opening. 11S regulators (also called PA26 (ref. 4), PA28 (ref. 5) and REG) are heptamers that stimulate 20S proteasome peptidase activity in vitro and may facilitate product release in vivo. Here we report the co-crystal structure of yeast 20S proteasome with the 11S regulator from Trypanosoma brucei (PA26). PA26 carboxy-terminal tails provide binding affinity by inserting into pockets on the 20S proteasome, and PA26 activation loops induce conformational changes in alpha-subunits that open the gate separating the proteasome interior from the intracellular environment. The reduction in processivity expected for an open conformation of the exit gate may explain the role of 11S regulators in the production of ligands for major histocompatibility complex class I molecules.

Figure 2.
Figure 2: Structure of PA26. a, PA26 heptamer coloured by monomer. b, Monomer coloured by secondary structure. This orientation corresponds to the magenta monomer in a. c, Proteasome-binding surface of the PA26 heptamer. Activation loops are yellow, C-terminal helix is red. View direction is from below structure in a. d, Alignment of T. brucei PA26 and human REG amino-acid sequences. Identical residues are shaded in pink. Disordered residues are indicated with a thin line. PA26/REG residues are structurally equivalent from the start of helix 2 to the C terminus as indicated. The alignment for helix 1 is tentative. The hexahistidine affinity tag inserted after the initiator methionine of PA26 is shown. Every tenth residue is marked with a dash (the first PA26 residue marked is Gln10). Residues that contact the 20S proteasome are indicated with blue triangles. The PA26 construct used in this study has a threonine in place of the authentic serine^4 at position 226.

Figure 4.
Figure 4: Mechanism of binding. a, Top view of the 20S proteasome -subunits with the molecular surface shown as a purple net. The seven pockets that receive PA26 C termini surround the central open gate. b, Side view of PA26 C-terminal residues (yellow) binding into a pocket. This view is a close up of the interface at the top left of Fig. 1b. The PA26 C-terminal carboxylate approaches the N terminus of 5 helix 1, which is in a vertical orientation in the lower part of this figure. 2F[o] - F[ c] density (0.8 times the r.m.s. deviation) was computed following torsion angle dynamics refinement in which the last 30 residues of PA26 were set to zero occupancy. Density for the last well-defined side chain of PA26, Arg 223, appears to connect the two segments of PA26 near the top of this figure.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 408, 115-120) copyright 2000.