2WZN

3d structure of TET3 from Pyrococcus horikoshii


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
354AA LONG HYPOTHETICAL OPERON PROTEIN FRVA354Pyrococcus horikoshiiMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 132.241α = 90
b = 132.241β = 90
c = 132.241γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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