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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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Related in: MedlinePlus

The proteolytic chamber.A, Open side view of the octamer. The front head-to-tail dimer has been removed. The top and bottom tetrameric rings are colored in blue and green, respectively. The β5–β6 and β16–β17 loops forming the two crown-shaped surfaces are colored in salmon and raspberry, respectively. To illustrate the size of the cavity, an Ala8-peptide was manually placed in extended conformation. B, Open top view of the octamer down the four-fold axis. For better clarity, the four N-terminal PRP domains of the top tetramer and the four C-terminal domain β16–β17 loops of the bottom tetramer have been removed. C, Same figure as in (B) tilted so that the active site entrance is visible. Catalytic pocket is highlighted in orange.
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pone-0004712-g006: The proteolytic chamber.A, Open side view of the octamer. The front head-to-tail dimer has been removed. The top and bottom tetrameric rings are colored in blue and green, respectively. The β5–β6 and β16–β17 loops forming the two crown-shaped surfaces are colored in salmon and raspberry, respectively. To illustrate the size of the cavity, an Ala8-peptide was manually placed in extended conformation. B, Open top view of the octamer down the four-fold axis. For better clarity, the four N-terminal PRP domains of the top tetramer and the four C-terminal domain β16–β17 loops of the bottom tetramer have been removed. C, Same figure as in (B) tilted so that the active site entrance is visible. Catalytic pocket is highlighted in orange.

Mentions: The 20 Å wide square-shaped channel, running along the four-fold axis through the entire complex, joins the equatorial two-fold axes into a 60 Å wide central cavern formed by association of the eight C-terminal domains (Figure 6A). Each active site, facing the central cavern, lies between three domains, the PRP and the lipocalin domains of one monomer, and the second lipocalin domain of a head-to-tail dimer (Figure 6C). The inside volume of the cavity is about 80,000 Å3, large enough to accomodate small unfolded peptides (Figure 6), and reminds those of other self-compartmentalizing proteases known to bury their active sites in an inner cavity. In the P. abyssi CubicO protease, the proteolytic chamber is separated from the access channels by two crown-shaped surfaces at about 10 Å of each side of the equatorial plane. These crowns are formed by two loops of opposite monomers joining at the same height (Figure 6A). The shape and size of the cavity are conserved in all CubicO proteases as shown by the structure modelling of the six other members of the family (Figure S2). Variability mainly concerns the access to the active site through the large and flexible loops forming the inside crowns appearing to function as substrate sieves (Figure 7).


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)

The proteolytic chamber.A, Open side view of the octamer. The front head-to-tail dimer has been removed. The top and bottom tetrameric rings are colored in blue and green, respectively. The β5–β6 and β16–β17 loops forming the two crown-shaped surfaces are colored in salmon and raspberry, respectively. To illustrate the size of the cavity, an Ala8-peptide was manually placed in extended conformation. B, Open top view of the octamer down the four-fold axis. For better clarity, the four N-terminal PRP domains of the top tetramer and the four C-terminal domain β16–β17 loops of the bottom tetramer have been removed. C, Same figure as in (B) tilted so that the active site entrance is visible. Catalytic pocket is highlighted in orange.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2651629&req=5

pone-0004712-g006: The proteolytic chamber.A, Open side view of the octamer. The front head-to-tail dimer has been removed. The top and bottom tetrameric rings are colored in blue and green, respectively. The β5–β6 and β16–β17 loops forming the two crown-shaped surfaces are colored in salmon and raspberry, respectively. To illustrate the size of the cavity, an Ala8-peptide was manually placed in extended conformation. B, Open top view of the octamer down the four-fold axis. For better clarity, the four N-terminal PRP domains of the top tetramer and the four C-terminal domain β16–β17 loops of the bottom tetramer have been removed. C, Same figure as in (B) tilted so that the active site entrance is visible. Catalytic pocket is highlighted in orange.
Mentions: The 20 Å wide square-shaped channel, running along the four-fold axis through the entire complex, joins the equatorial two-fold axes into a 60 Å wide central cavern formed by association of the eight C-terminal domains (Figure 6A). Each active site, facing the central cavern, lies between three domains, the PRP and the lipocalin domains of one monomer, and the second lipocalin domain of a head-to-tail dimer (Figure 6C). The inside volume of the cavity is about 80,000 Å3, large enough to accomodate small unfolded peptides (Figure 6), and reminds those of other self-compartmentalizing proteases known to bury their active sites in an inner cavity. In the P. abyssi CubicO protease, the proteolytic chamber is separated from the access channels by two crown-shaped surfaces at about 10 Å of each side of the equatorial plane. These crowns are formed by two loops of opposite monomers joining at the same height (Figure 6A). The shape and size of the cavity are conserved in all CubicO proteases as shown by the structure modelling of the six other members of the family (Figure S2). Variability mainly concerns the access to the active site through the large and flexible loops forming the inside crowns appearing to function as substrate sieves (Figure 7).

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