2QMI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2009) Plos One 4: e4712-e4712

  • DOI: 10.1371/journal.pone.0004712

  • 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 fo ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pbp related beta-lactamase
A, B, C, D, E, F, G, H
447Pyrococcus abyssi (strain GE5 / Orsay)Gene Names: pbp
Find proteins for Q9V2D6 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2D6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DO3
Query on DO3

Download SDF File 
Download CCD File 
E, F, G, H
10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
C17 H32 N4 O7
IQUHNCOJRJBMSU-CQSZACIVSA-N
 Ligand Interaction
LU
Query on LU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
LUTETIUM (III) ION
LU
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 100.940α = 72.17
b = 105.630β = 66.51
c = 112.920γ = 81.39
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
XDSdata reduction
PDB_EXTRACTdata extraction
CNSrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance