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PDBsum entry 2cf4
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References listed in PDB file
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Key reference
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Title
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An archaeal peptidase assembles into two different quaternary structures: a tetrahedron and a giant octahedron.
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Authors
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G.Schoehn,
F.M.Vellieux,
M.Asunción durá,
V.Receveur-Bréchot,
C.M.Fabry,
R.W.Ruigrok,
C.Ebel,
A.Roussel,
B.Franzetti.
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Ref.
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J Biol Chem, 2006,
281,
36327-36337.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
36327-36337)
copyright 2006.
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Secondary reference #1
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Title
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Tetrahedral aminopeptidase: a novel large protease complex from archaea.
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Authors
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B.Franzetti,
G.Schoehn,
J.F.Hernandez,
M.Jaquinod,
R.W.Ruigrok,
G.Zaccai.
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Ref.
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EMBO J, 2002,
21,
2132-2138.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Alignment of two assigned bacterial and archaeal M42
aminopeptidase sequences with the sequence of the TET protein
from Halobacterium sp. The residues that are conserved in at
least two sequences are boxed. L.l, Lactococcus lactis,
DDBJ/EMBL/GenBank accession No. X81089; P.h, Pyrococcus
horikoshii, DDBJ/EMBL/GenBank accession No. AP000006; H.s,
Halobacterium sp. NRC1, DDBJ/EMBL/GenBank accession No.
AE005064. Crosses indicate the amino acids that are putatively
involved in metal binding, and asterisks indicate the putative
active sites residues (according to MEROPS, a protease databank
available online at: http://www.merops.ac.uk).
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Figure 4.
Figure 4 Substrate specificity of TET. The hydrolytic reactions
were measured by using chromogenic (pNA) or fluorogenic (AMC)
monoacyl compounds as described in Materials and methods.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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