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Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.

Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C - PLoS ONE (2009)

Bottom Line: A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites.Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism.We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

View Article: PubMed Central - PubMed

Affiliation: Centre de Recherche des Cordeliers, LRMA, INSERM UMR-S 872, Université Pierre et Marie Curie, Paris, France.

ABSTRACT
Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

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Primary structure of the CubicO proteases.Schematic representation of the CubicO protease sequences. The PRP (serine protease) α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in orange and the lipocalin domain in salmon. Numbering refers to the Pab87 sequence. The three PRP conserved motifs are indicated in black, the three CubicO specific motifs in red.
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pone-0004712-g001: Primary structure of the CubicO proteases.Schematic representation of the CubicO protease sequences. The PRP (serine protease) α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in orange and the lipocalin domain in salmon. Numbering refers to the Pab87 sequence. The three PRP conserved motifs are indicated in black, the three CubicO specific motifs in red.

Mentions: Intracellular protein breakdown is a universal process that implicates protein degradation carried out by high-molecular-weight self-compartmentalizing proteases [1], [2]. They belong to different MEROPS families [3] but have converged towards the same barrel-shaped architecture. Compartmentalization confines the peptidase activity to inner cavities only accessible to unfolded polypeptides. Initial proteolysis is fulfilled by energy-dependent proteasome in eukaryotes and archaea [4] or by the equivalent bacterial counterparts, HslVU [5], ClpAP [6], or Lon [7], which generate peptides of about 10 amino acids long. In addition to the energy-dependent proteasome systems, energy-independent protease complexes have been described to further process and degrade the peptides produced by proteasomes. Organisms diverged in terms of peptide hydrolysis processes and have their own specific pool of different energy-independent proteases that functionally complements the proteasome activity [8]. Structural studies of such complexes, that putatively take part in the degradation of small oligopeptides, reveal several types of organization. The 720 kDa Tricorn protease from Thermoplasma acidophilum contains six subunits associated into rings with D3 symmetry and possesses trypsin- and chymotrypsin-like activities [9]. A larger assembly has been observed in vivo for Tricorn where 20 hexamers form a 14.6 MDa icosahedral capsid, whose physiological role is unknown [10]. The TET aminopeptidases are present in organisms where Tricorn is not found [11]. The crystal structures of archaeal Pyrococcus horikoshii PhTET1 and PhTET2 have revealed that these proteases adopt a tetrahedral shape containing twelve subunits [12], [13]. Like for Tricorn, TET can form a supramolecular assembly of 800 kDa composed of 24 subunits and referred to as octahedron, only observed in vivo yet [14]. TppII is the only energy-independent self-compartmentalizing protease found exclusively in eukaryotes and consists of a particle of more than 1 MDa displaying both exo- and endo-proteolytic activities. TppII adopts a toroidal shape of 28 Å large and 60 Å long revealed by electron microscopy data [15] and is considered as the eukaryotic counterpart of Tricorn. Finally, the DppA d-aminopeptidase from Bacillus subtilis was the only example of d-stereospecific self-compartmentalizing protease described so far [16]. DppA is a homodecameric particule with D5 symmetry only found in bacteria and archaea. Here, we report the structure of a novel self-compartmentalizing protease, the Pab87 protein from the hyperthermophilic euryarchaeon Pyrococcus abyssi. Pab87 is a serine protease belonging to the MEROPS S12 family and displays sequence similarity with penicillin-recognizing proteins, termed PRP (Figure 1). This proteolytic complex of 0.4 MDa adopts a D4 barrel-shaped oligomeric architecture with a central channel and an internal cavity. Furthermore, protein Pab87 is, like DppA, d-stereospecific as shown by activity assays and is proposed to play a role in the processing of environmental d-amino acid containing peptides.


Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.

Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C - PLoS ONE (2009)

Primary structure of the CubicO proteases.Schematic representation of the CubicO protease sequences. The PRP (serine protease) α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in orange and the lipocalin domain in salmon. Numbering refers to the Pab87 sequence. The three PRP conserved motifs are indicated in black, the three CubicO specific motifs in red.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2651629&req=5

pone-0004712-g001: Primary structure of the CubicO proteases.Schematic representation of the CubicO protease sequences. The PRP (serine protease) α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in orange and the lipocalin domain in salmon. Numbering refers to the Pab87 sequence. The three PRP conserved motifs are indicated in black, the three CubicO specific motifs in red.
Mentions: Intracellular protein breakdown is a universal process that implicates protein degradation carried out by high-molecular-weight self-compartmentalizing proteases [1], [2]. They belong to different MEROPS families [3] but have converged towards the same barrel-shaped architecture. Compartmentalization confines the peptidase activity to inner cavities only accessible to unfolded polypeptides. Initial proteolysis is fulfilled by energy-dependent proteasome in eukaryotes and archaea [4] or by the equivalent bacterial counterparts, HslVU [5], ClpAP [6], or Lon [7], which generate peptides of about 10 amino acids long. In addition to the energy-dependent proteasome systems, energy-independent protease complexes have been described to further process and degrade the peptides produced by proteasomes. Organisms diverged in terms of peptide hydrolysis processes and have their own specific pool of different energy-independent proteases that functionally complements the proteasome activity [8]. Structural studies of such complexes, that putatively take part in the degradation of small oligopeptides, reveal several types of organization. The 720 kDa Tricorn protease from Thermoplasma acidophilum contains six subunits associated into rings with D3 symmetry and possesses trypsin- and chymotrypsin-like activities [9]. A larger assembly has been observed in vivo for Tricorn where 20 hexamers form a 14.6 MDa icosahedral capsid, whose physiological role is unknown [10]. The TET aminopeptidases are present in organisms where Tricorn is not found [11]. The crystal structures of archaeal Pyrococcus horikoshii PhTET1 and PhTET2 have revealed that these proteases adopt a tetrahedral shape containing twelve subunits [12], [13]. Like for Tricorn, TET can form a supramolecular assembly of 800 kDa composed of 24 subunits and referred to as octahedron, only observed in vivo yet [14]. TppII is the only energy-independent self-compartmentalizing protease found exclusively in eukaryotes and consists of a particle of more than 1 MDa displaying both exo- and endo-proteolytic activities. TppII adopts a toroidal shape of 28 Å large and 60 Å long revealed by electron microscopy data [15] and is considered as the eukaryotic counterpart of Tricorn. Finally, the DppA d-aminopeptidase from Bacillus subtilis was the only example of d-stereospecific self-compartmentalizing protease described so far [16]. DppA is a homodecameric particule with D5 symmetry only found in bacteria and archaea. Here, we report the structure of a novel self-compartmentalizing protease, the Pab87 protein from the hyperthermophilic euryarchaeon Pyrococcus abyssi. Pab87 is a serine protease belonging to the MEROPS S12 family and displays sequence similarity with penicillin-recognizing proteins, termed PRP (Figure 1). This proteolytic complex of 0.4 MDa adopts a D4 barrel-shaped oligomeric architecture with a central channel and an internal cavity. Furthermore, protein Pab87 is, like DppA, d-stereospecific as shown by activity assays and is proposed to play a role in the processing of environmental d-amino acid containing peptides.

Bottom Line: A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites.Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism.We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

View Article: PubMed Central - PubMed

Affiliation: Centre de Recherche des Cordeliers, LRMA, INSERM UMR-S 872, Université Pierre et Marie Curie, Paris, France.

ABSTRACT
Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

Show MeSH
Related in: MedlinePlus