2QMI

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

• PDB DOI:  https://doi.org/10.2210/pdb2QMI/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-16 Released: 2008-07-22 
• Deposition Author(s): Delfosse, V., Girard, E., Moulinier, L., Schultz, P., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

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

• PubMed: 19266066 
• DOI: https://doi.org/10.1371/journal.pone.0004712
• Primary Citation of Related Structures:  
  2QMI


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 408.62 kDa 
• Atom Count: 30,882 
• Modelled Residue Count: 3,573 
• Deposited Residue Count: 3,576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pbp related beta-lactamase	A, B, C, D, E, F, G, H	447	Pyrococcus abyssi	Mutation(s): 0  Gene Names: pbp EC: 3.5.2.6
UniProt
Find proteins for Q9V2D6 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2D6  Go to UniProtKB:  Q9V2D6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DO3	AA [auth G], CA [auth H], S [auth E], W [auth F]	10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID C17 H32 N4 O7 IQUHNCOJRJBMSU-CQSZACIVSA-N
LU	BA [auth H], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], T [auth F], U [auth F], V [auth F], X [auth G], Y [auth G], Z [auth G]	LUTETIUM (III) ION Lu PSDMOPINLDTFSZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.94	α = 72.17
b = 105.63	β = 66.51
c = 112.92	γ = 81.39

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Delfosse, V., Girard, E., Moulinier, L., Schultz, P., Mayer, C.

Revision History  

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