4X8I

de novo crystal structure of the Pyrococcus Furiosus TET3 aminopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1038/srep20876
  • Primary Citation of Related Structures:  
    4X8I

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysyl aminopeptidase
A, B, C
346Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1861
EC: 3.4.11.15
UniProt
Find proteins for Q8TZW4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZW4 
Go to UniProtKB:  Q8TZW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DO3
Query on DO3

Download Ideal Coordinates CCD File 
X [auth C]10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID
C17 H32 N4 O7
IQUHNCOJRJBMSU-CQSZACIVSA-N
GD
Query on GD

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
Q [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
R [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
S [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.908α = 90
b = 203.908β = 90
c = 112.443γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SHELXphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Centre Nationale de la Recherche ScientifiqueFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 2.0: 2019-11-20
    Changes: Advisory, Atomic model, Derived calculations
  • Version 2.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations