Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.42 kDa 
• Atom Count: 2871 
• Residue Count: 338 
• Unique protein chains: 1

2WZN

3d structure of TET3 from Pyrococcus horikoshii

• DOI: 10.2210/pdb2WZN/pdb
• Entry: 2WZN supersedes: 2VPU

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-12-01 Released: 2010-11-03 
• Deposition Author(s): Rosenbaum, E., Dura, M.A., Vellieux, F.M., Franzetti, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.175 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 

Literature

The Structural and Biochemical Characterizations of a Novel Tet Peptidase Complex from Pyrococcus Horikoshii Reveal an Integrated Peptide Degradation System in Hyperthermophilic Archaea.

Dura, M.A., Rosenbaum, E., Larabi, A., Gabel, F., Vellieux, F.M., Franzetti, B.

(2009) Mol Microbiol 72: 26

• PubMed: 19291145 
• DOI: 10.1111/j.1365-2958.2009.06600.x
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The structure of a 468 kDa peptidase complex from the hyperthermophile Pyrococcus horikoshii has been solved at 1.9 A resolution. The monomer contains the M42 peptidase typical catalytic domain, and a dimerization domain that allows the formation of dimers that assemble as a 12-subunit self-compartmentalized tetrahedron, similar to those described for the TET peptidases. The biochemical analysis shows that the enzyme is cobalt-activated and cleaves peptides by a non-processive mechanism. Consequently, this protein represents the third TET peptidase complex described in P. horikoshii, thereby called PhTET3. It is a lysyl aminopeptidase with a strong preference for basic residues, which are poorly cleaved by PhTET1 and PhTET2. The structural analysis of PhTET3 and its comparison with PhTET1 and PhTET2 unravels common features explaining the general mode of action of the TET molecular machines as well as differences that can be associated with strong substrate discriminations. The question of the stability of the TET assemblies under extreme temperatures has been addressed. PhTET3 displays its maximal activity at 95 degrees C and small-angle neutron scattering experiments at 90 degrees C demonstrate the absence of quaternary structure alterations after extensive incubation times. In conclusion, PhTETs are complementary peptide destruction machines that may play an important role in the metabolism of P. horikoshii.

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Related Citations: 

• An Archaeal Peptidase Assembles Into Two Different Quaternary Structures: A Tetrahedron and a Giant Octahedron.
  Schoehn, G., Vellieux, F.M.D., Asuncion Dura, M., Receveur-Brechot, V., Fabry, C.M.S., Ruigrok, R.W.H., Ebel, C., Roussel, A., Franzetti, B.
  (2006) J Biol Chem 281: 36327

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Organizational Affiliation: 

Institut de Biologie Structurale J.-P. Ebel, UMR 5075 CNRS-CEA-UJF, 41 rue Jules Horowitz, 38027 Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
354AA LONG HYPOTHETICAL OPERON PROTEIN FRV	A	354	Pyrococcus horikoshii	Mutation(s): 0
Find proteins for O59485 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59485  Go to UniProtKB:  O59485

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.175 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.241	α = 90
b = 132.241	β = 90
c = 132.241	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-01 
• Released Date: 2010-11-03 
Deposition Author(s): Rosenbaum, E., Dura, M.A., Vellieux, F.M., Franzetti, B.
• This entry supersedes: 2VPU

Revision History 

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance