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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

Secondary structure assignationfor A, the N- and B, the C-terminal domains of the P. abyssi Pab87 monomer, color coded according to Figure 1 (the PRP α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in light orange and the lipocalin domain in salmon). The active site is located by a star in (A).
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pone-0004712-g004: Secondary structure assignationfor A, the N- and B, the C-terminal domains of the P. abyssi Pab87 monomer, color coded according to Figure 1 (the PRP α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in light orange and the lipocalin domain in salmon). The active site is located by a star in (A).

Mentions: The 50.4 kDa monomer of Pab87 consists of two structural domains, an N-terminal PRP domain associated to a C-terminal lipocalin domain that plays a crucial role in the octamerization and in the active site compartmentalization (Figure 2A). The N-terminal domain structure follows the pattern of the known PRP structures, composed of two regions, one α/β and one all-helical region with six helices. The α/β region is discontinuous in sequence and consists of a main eight-stranded antiparallel β-sheet flanked by three helices. The C-terminal domain is connected to the N-terminal domain by a small helix, folded back onto the last helix of the N-terminal domain. The Pab87 C-terminal domain presents a typical lipocalin superfold [18] that consists of an α-helix and an eight-stranded antiparallel β-barrel (Figure 4). This N-terminal α-helix closes off the top of the barrel, in vicinity of the PRP domain. Like for all lipocalins, the interior of the barrel is coated with hydrophobic residues. The tunnel observed in the lipocalins is replaced by a small recess at the bottom of the calyx. As lipocalins were first discovered in eukaryotes, and more recently in bacteria [19], the Pab87 C-terminal domain provides the first example of an archaeal lipocalin.


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)

Secondary structure assignationfor A, the N- and B, the C-terminal domains of the P. abyssi Pab87 monomer, color coded according to Figure 1 (the PRP α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in light orange and the lipocalin domain in salmon). The active site is located by a star in (A).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004712-g004: Secondary structure assignationfor A, the N- and B, the C-terminal domains of the P. abyssi Pab87 monomer, color coded according to Figure 1 (the PRP α/β and all-helical regions are in light blue and cyan, respectively, the linking helix in light orange and the lipocalin domain in salmon). The active site is located by a star in (A).
Mentions: The 50.4 kDa monomer of Pab87 consists of two structural domains, an N-terminal PRP domain associated to a C-terminal lipocalin domain that plays a crucial role in the octamerization and in the active site compartmentalization (Figure 2A). The N-terminal domain structure follows the pattern of the known PRP structures, composed of two regions, one α/β and one all-helical region with six helices. The α/β region is discontinuous in sequence and consists of a main eight-stranded antiparallel β-sheet flanked by three helices. The C-terminal domain is connected to the N-terminal domain by a small helix, folded back onto the last helix of the N-terminal domain. The Pab87 C-terminal domain presents a typical lipocalin superfold [18] that consists of an α-helix and an eight-stranded antiparallel β-barrel (Figure 4). This N-terminal α-helix closes off the top of the barrel, in vicinity of the PRP domain. Like for all lipocalins, the interior of the barrel is coated with hydrophobic residues. The tunnel observed in the lipocalins is replaced by a small recess at the bottom of the calyx. As lipocalins were first discovered in eukaryotes, and more recently in bacteria [19], the Pab87 C-terminal domain provides the first example of an archaeal lipocalin.

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