PDBsum entry 3jrm

Hydrolase/hydrolase activator

PDB id: 3jrm

Contents

Protein chains

(+ 1 more) 227 a.a. *

(+ 1 more) 203 a.a. *

(+ 1 more) 218 a.a. *

* Residue conservation analysis

PDB id:

3jrm

Name:

Hydrolase/hydrolase activator

Title:

Crystal structure of archaeal 20s proteasome in complex with mutated p26 activator

Structure:

Proteasome subunit alpha. Chain: a, b, c, d, e, f, g. Synonym: multicatalytic endopeptidase complex subunit alpha. Engineered: yes. Proteasome subunit beta. Chain: h, i, j, k, l, m, n. Synonym: multicatalytic endopeptidase complex subunit beta. Engineered: yes. Proteasome activator protein pa26.

Source:

Thermoplasma acidophilum. Organism_taxid: 2303. Gene: psma, ta1288. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: psmb, ta0612. Trypanosoma brucei. Organism_taxid: 5691. Expression_system_taxid: 562

Resolution:

2.90Å R-factor: 0.202 R-free: 0.233

Authors:

B.M.Stadtmueller,F.G.Whitby,C.P.Hill

Key ref:

B.M.Stadtmueller et al. (2010). Structural models for interactions between the 20S proteasome and its PAN/19S activators. J Biol Chem, 285, 13-17. PubMed id: 19889631 DOI: 10.1074/jbc.C109.070425

Date:

08-Sep-09 Release date: 03-Nov-09

Protein chains

P25156  (PSA_THEAC) -  Proteasome subunit alpha from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

Seq: 233 a.a.

Struc: 227 a.a.

Protein chains

P28061  (PSB_THEAC) -  Proteasome subunit beta from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

Seq: 211 a.a.

Struc: 203 a.a.

Protein chains

Q9U8G2  (Q9U8G2_9TRYP) -  Proteasome activator protein PA26 (Fragment) from Trypanosoma brucei

Seq: 231 a.a.

Struc: 218 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.

DOI no: 10.1074/jbc.C109.070425

J Biol Chem 285:13-17 (2010)

PubMed id: 19889631

Structural models for interactions between the 20S proteasome and its PAN/19S activators.

B.M.Stadtmueller, K.Ferrell, F.G.Whitby, A.Heroux, H.Robinson, D.G.Myszka, C.P.Hill.

ABSTRACT

Proteasome activity is regulated by sequestration of its proteolytic centers in a barrel-shaped structure that limits substrate access. Substrates enter the proteasome by means of activator complexes that bind to the end rings of proteasome alpha subunits and induce opening of an axial entrance/exit pore. The PA26 activator binds in a pocket on the proteasome surface using main chain contacts of its C-terminal residues and uses an internal activation loop to trigger gate opening by repositioning the proteasome Pro-17 reverse turn. Subunits of the unrelated PAN/19S activators bind with their C termini in the same pockets but can induce proteasome gate opening entirely from interactions of their C-terminal peptides, which are reported to cause gate opening by inducing a rocking motion of proteasome alpha subunits rather than by directly contacting the Pro-17 turn. Here we report crystal structures and binding studies of proteasome complexes with PA26 constructs that display modified C-terminal residues, including those corresponding to PAN. These findings suggest that PA26 and PAN/19S C-terminal residues bind superimposably and that both classes of activator induce gate opening by using direct contacts to residues of the proteasome Pro-17 reverse turn. In the case of the PAN and 19S activators, a penultimate tyrosine/phenylalanine residue contacts the proteasome Gly-19 carbonyl oxygen to stabilize the open conformation.

Selected figure(s)

Figure 1.
Structures of PA26-proteasome complexes. A, overall structure with one PA26 subunit colored blue and its three C-terminal residues in space-filling representation. Proteasome subunits that form the corresponding binding pocket are pink and gray (white in subsequent panels). B, close-up showing main chain hydrogen-bonding interactions of the PA26 C-terminal residues (31). C, sequences and structures of PA26 (31) and variants described in this work shown after overlap on the proteasome structures. D, the penultimate Tyr-230 residue contacts Gly-19 to reposition the Pro-17 turn. Distances between Tyr-230-OH and Gly-19-O in closed (red; modeled) and open (green; observed) conformations are shown. Pro-17 undergoes an apparent movement of ∼1 Å. H0, helix 0. E, binding pocket with proteasome shown as a semitransparent molecular surface. Conserved residues whose side chains contact the activator C-terminal residues are indicated. F, V230F penultimate phenylalanine interactions observed with Gly-19 in the open conformation (pink) and modeled in the closed conformation (blue). To best describe contacts, riding hydrogen atoms were included in determined structures and assessed with MolProbity (36).

Figure 2.
PA26-proteasome binding studies. A–E, biosensorgrams showing concentration-dependent binding of PA26 variants to the S. cerevisiae proteasome and calculated average dissociation constants (K[D]). Binding to an IgG control surface was negligible (data not shown). RU, response units. F, kinetic plot of k[a] versus k[d] where diagonals represent K[D], and values for each PA26 variant are shown as spots. The K[D] standard deviation is less than the size of the spots.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2010, 285, 13-17) copyright 2010.