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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 CubicO particle.Structural regions are color coded as in Figure 1. A, Ribbon representation of the head-to-tail dimer structure forming the edges of the cubic-shaped octamer. B, side view along and C, top view perpendicular to the four-fold axis of the octamer. The central ring formed by the C-terminal domains represents one third of the total height. D, Fitting of cryo-EM map shown in transparent solid surface with the X-ray structure.
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pone-0004712-g002: The CubicO particle.Structural regions are color coded as in Figure 1. A, Ribbon representation of the head-to-tail dimer structure forming the edges of the cubic-shaped octamer. B, side view along and C, top view perpendicular to the four-fold axis of the octamer. The central ring formed by the C-terminal domains represents one third of the total height. D, Fitting of cryo-EM map shown in transparent solid surface with the X-ray structure.

Mentions: The Pab87 structure was determined at 2.2 Å resolution using the single-wavelength anomalous dispersion method with anomalous signal of a high-phasing-power lanthanide derivative, the Lu-HPDO3A complex (Table 1) [17]. Pab87 is the first characterized member of a new self-compartmentalizing protease family, referred to as CubicO proteases as they display a cubic-shaped octameric form (Figure 2). The molecular mass of the macromolecular assembly was confirmed using analytical ultracentrifugation (391±10 kDa). The crystal structure of the P. abyssi CubicO protease (Pab87) reveals a 422 symmetry, where the eight monomers are arranged in a barrel-shaped architecture. In the protease complex, monomers associate through a non-crystallographic four-fold axis to form two stacked tetramers that are themselves related by a non-crystallographic two-fold axis perpendicular to the latter. The C-terminal domains interdigitate and form a central ring of one third of the total height of the octamer, playing a central role in this oligomerization (Figure 2B). Moreover, cryo-electron microscopy data show that Pab87 adopts the same octameric structure in solution (Figure 2D).


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 CubicO particle.Structural regions are color coded as in Figure 1. A, Ribbon representation of the head-to-tail dimer structure forming the edges of the cubic-shaped octamer. B, side view along and C, top view perpendicular to the four-fold axis of the octamer. The central ring formed by the C-terminal domains represents one third of the total height. D, Fitting of cryo-EM map shown in transparent solid surface with the X-ray structure.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004712-g002: The CubicO particle.Structural regions are color coded as in Figure 1. A, Ribbon representation of the head-to-tail dimer structure forming the edges of the cubic-shaped octamer. B, side view along and C, top view perpendicular to the four-fold axis of the octamer. The central ring formed by the C-terminal domains represents one third of the total height. D, Fitting of cryo-EM map shown in transparent solid surface with the X-ray structure.
Mentions: The Pab87 structure was determined at 2.2 Å resolution using the single-wavelength anomalous dispersion method with anomalous signal of a high-phasing-power lanthanide derivative, the Lu-HPDO3A complex (Table 1) [17]. Pab87 is the first characterized member of a new self-compartmentalizing protease family, referred to as CubicO proteases as they display a cubic-shaped octameric form (Figure 2). The molecular mass of the macromolecular assembly was confirmed using analytical ultracentrifugation (391±10 kDa). The crystal structure of the P. abyssi CubicO protease (Pab87) reveals a 422 symmetry, where the eight monomers are arranged in a barrel-shaped architecture. In the protease complex, monomers associate through a non-crystallographic four-fold axis to form two stacked tetramers that are themselves related by a non-crystallographic two-fold axis perpendicular to the latter. The C-terminal domains interdigitate and form a central ring of one third of the total height of the octamer, playing a central role in this oligomerization (Figure 2B). Moreover, cryo-electron microscopy data show that Pab87 adopts the same octameric structure in solution (Figure 2D).

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