4X8I

de novo crystal structure of the Pyrococcus Furiosus TET3 aminopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites.

Colombo, M.Girard, E.Franzetti, B.

(2016) Sci Rep 6: 20876-20876

  • DOI: 10.1038/srep20876

  • PubMed Abstract: 
  • TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and ...

    TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn(2+), hyperthermophilic TETs prefers Co(2+). Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.


    Organizational Affiliation

    CNRS, IBS, F-38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysyl aminopeptidase
A, B, C
346Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
EC: 3.4.11.15
Find proteins for Q8TZW4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8TZW4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DO3
Query on DO3

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Download CCD File 
C
10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
C17 H32 N4 O7
IQUHNCOJRJBMSU-CQSZACIVSA-N
 Ligand Interaction
GD
Query on GD

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Download CCD File 
A, B, C
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
A, B, C
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 203.908α = 90.00
b = 203.908β = 90.00
c = 112.443γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
SHELXphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-12-10 
  • Released Date: 2016-02-10 
  • Deposition Author(s): Colombo, M.

Funding OrganizationLocationGrant Number
Centre Nationale de la Recherche ScientifiqueFrance--

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references