PDBsum entry: 2gop

Hydrolase

PDB-id: 2gop

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

320 a.a. *

304 a.a. *

Waters ×242

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2gop

Name:

Hydrolase

Title:

The beta-propeller domain of the trilobed protease from pyrococcus furiosus reveals an open velcro topology

Structure:

Trilobed protease. Chain: a, b. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

Chain A: Q8U3Y3 (Q8U3Y3_PYRFU)

Seq:
Struc:
	Seq:
	Struc:
Seq:		620 a.a.
Struc:		320 a.a.

Chain B: Q8U3Y3 (Q8U3Y3_PYRFU)

Seq:

Struc:

Seq:

Struc:

Seq:

620 a.a.

Struc:

304 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

2.00Å

R-factor:

0.210

R-free:

0.258

Authors:

J.Bosch,T.Tamura,N.Tamura,W.Baumeister,L.-O.Essen

Key ref:

J.Bosch et al. (2007). The beta-propeller domain of the trilobed protease from Pyrococcus furiosus reveals an open Velcro topology.. Acta Crystallogr D Biol Crystallogr, 63, 179-187. [PubMed id: 17242511] [DOI: 10.1107/S0907444906045471]

Date:

13-Apr-06

Release date:

23-Jan-07

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1107/S0907444906045471

Acta Crystallogr D Biol Crystallogr 63:179-187 (2007)

PubMed id: 17242511

The beta-propeller domain of the trilobed protease from Pyrococcus furiosus reveals an open Velcro topology.

J.Bosch, T.Tamura, N.Tamura, W.Baumeister, L.O.Essen.

ABSTRACT

In the proteolytic pathway of prokaryotic and eukaryotic organisms, proteins tagged for proteolysis are firstly shredded into smaller peptides by compartmentalized proteases such as the proteasome complex. Accordingly, a variety of downstream proteases have evolved to further hydrolyze these peptides to the level of free amino acids. In the search for such downstream proteases, a high-molecular-weight protease complex called trilobed protease (TLP) was recently discovered in the archaeon Pyroccocus furiosus. The crystal structure of the N-terminal beta-propeller domain of the trilobed protease at 2 A resolution shows that the trilobed protease utilizes this accessory domain to control substrate access to the active site. Modelling of the intact TLP monomer suggests that this protease has an additional side entrance to its active site as in the DPP-IV or tricorn protease complexes.

Selected figure(s)

Figure 3.
Figure 3 (a) Three-dimensional representation of a hypothetical model of the intact trilobed protease. Structure prediction of the / -hydrolase domain was performed using the LIBELLULA server (Juan et al., 2003[Juan, D., Grana, O., Pazos, F., Fariselli, P., Casadio, R. & Valencia, A. (2003). Proteins, 50, 600-608.]) and is shown in brown. The -propeller domain is depicted as in the previous figures. Both domains were fitted using the program TOP (Lu, 2000[Lu, G. (2000). J. Appl. Cryst. 33, 176-183.]) according to the overall structure of prolyl oligopeptidase (Fülöp et al., 1998[Fülöp, V., Bocskei, Z. & Polgar, L. (1998). Cell, 94, 161-170.]). Residues of the active site are shown as green spheres. (b) Schematic overview of possible substrate pathways in the monomeric trilobed enzyme. Green arrows represent substrate access to the active site; the catalytic domain is represented as a cone-shaped domain and the -propeller domain is colour coded by individual blades. The first model represents a diffuse only model, where the pore cannot be widened, and the second model allows a limited widening of the central pore; both cases are applicable to the Velcro-type closures of -propeller domains. The third and the fourth model result in larger movements of the -propeller domain and are limited to non-Velcro-type -propellers, allowing a larger breathing mechanism for the uptake of larger substrates. The last model is a combination of the breathing mechanism and an additional domain movement, allowing much larger substrates to access the catalytic site via the side entrance.

Figure 4.
Figure 4 Comparison of TLP- with other -propeller domains from compartmentalized proteases. (a) Ribbon diagram of TLP- as viewed along the sevenfold pseudo-symmetry axis. The nine aspartate residues forming the negative ring at the entrance to the channel are highlighted as a ball-and-stick model. (b) Electrostatic surface representation of TLP- in top, bottom and cut-open side views. Negative surface charges are coloured red and positive charges blue. (c) Surface representation (colour codes: aromatic, green; aliphatic, yellow; polar, cyan; charged, grey) showing the interior side of the channel of the superimposed structures of TLP- (I), POP (II), TRI- 7 (III) and DPP-IV (IV) from the bottom view.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 179-187) copyright 2007.

Figures were selected by the author.