2QMI

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

Summary for 2QMI

• Entry DOI: 10.2210/pdb2qmi/pdb
• Descriptor: Pbp related beta-lactamase, LUTETIUM (III) ION, 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID, ... (4 entities in total)
• Functional Keywords: pab87, octamer, lu-hpdo3a, pbp, archaea, hydrolase
• Biological source: Pyrococcus abyssi
• Total number of polymer chains: 8
• Total formula weight: 408619.24

Authors

Delfosse, V.,Girard, E.,Moulinier, L.,Schultz, P.,Mayer, C. (deposition date: 2007-07-16, release date: 2008-07-22, Last modification date: 2024-02-21)

Primary citation

Delfosse, V.,Girard, E.,Birck, C.,Delmarcelle, M.,Delarue, M.,Poch, O.,Schultz, P.,Mayer, C.
Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family
Plos One, 4:e4712-e4712, 2009

PubMed 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.

PubMed: 19266066
DOI: 10.1371/journal.pone.0004712

Experimental method

X-RAY DIFFRACTION (2.2 Å)