PDBsum entry 2cf4

Hydrolase

PDB id: 2cf4

Contents

Protein chain

330 a.a. *

Metals

_CO ×2

* Residue conservation analysis

PDB id:

2cf4

Name:

Hydrolase

Title:

Pyrococcus horikoshii tet1 peptidase can assemble into a tetrahedron or a large octahedral shell

Structure:

Protein ph0519. Chain: a. Synonym: phtet1-12s. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dodecamer (from PDB file)

Resolution:

3.08Å R-factor: 0.256 R-free: 0.332

Authors:

F.M.D.Vellieux,G.Schoehn,M.A.Dura,A.Roussel,B.Franzetti

Key ref:

G.Schoehn et al. (2006). An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron. J Biol Chem, 281, 36327-36337. PubMed id: 16973604 DOI: 10.1074/jbc.M604417200

Date:

15-Feb-06 Release date: 14-Sep-06

Protein chain

O58255  (O58255_PYRHO) -  Uncharacterized protein from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 332 a.a.

Struc: 330 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.11.- - ?????

DOI no: 10.1074/jbc.M604417200

J Biol Chem 281:36327-36337 (2006)

PubMed id: 16973604

An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.

G.Schoehn, F.M.Vellieux, M.Asunción Durá, V.Receveur-Bréchot, C.M.Fabry, R.W.Ruigrok, C.Ebel, A.Roussel, B.Franzetti.

ABSTRACT

Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.

Selected figure(s)

Figure 2.
FIGURE 2. Secondary structure elements of PhTET1. A, schematic representation of the PhTET1-12s dimer along the 2-fold symmetry axis, as it appears viewed from the exterior of the dodecameric complex (see Fig. 3A, left). In each monomer, catalytic domains are colored in orange and magenta, dimerization domains in blue, and cobalt ions in green. Dimerization is achieved through formation of contacts between the dimerization domain of one monomer and a mixed four-stranded -sheet (magenta) present in the catalytic domain of the other monomer. B, multiple sequence alignment indicating the secondary structure elements in PhTET1, assigned with DSSP (38), colored as in A. The abbreviations and GenBank^TM accession numbers of the sequences are as follows: TET1, P. horikoshii TET1 (AP000002); TET2, P. horikoshii TET2 (AP000006); YsdC, B. subtilis YsdC protein (Z75208, Z99118); and AAP, aminopeptidase Ap1 from Vibrio proteolyticus (M85159, Z11993). The conserved metal-binding residues are indicated by a ball and the catalytic residues by a star (according to the MEROPS data base assignment).

Figure 4.
FIGURE 4. Dimer structure in the two PhTET1 complexes. A, ribbon representation of a dimer extracted from the tetracosamer quasi-atomic model (blue) superimposed to a dimer from the dodecamer x-ray structure (red). Cobalt ions are shown as spheres. The bottom monomers of each dimer were forced to match, hence the stereo picture illustrates the rotation of 14° of the upper PhTET1-24s monomer with respect to the center of mass of the PhTET1-12s dimer. A and Fig. 2A are related by a 90° rotation around the vertical axis. B, cut open surface representations of the PhTET1 edifices showing the position of one dimer in the tetrahedral complex (top) and in the octahedral assembly (bottom). The dimers are depicted and oriented as in A.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 36327-36337) copyright 2006.

Figures were selected by an automated process.