6GDF

DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 600 BAR OF HYDROSTATIC PRESSURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pressure-induced activation of latent dihydroorotase from Aquifex aeolicus as revealed by high pressure protein crystallography.

Prange, T.Girard, E.Fourme, R.Dhaussy, A.C.Edwards, B.Vaishnav, A.Patel, C.Guy-Evans, H.Herve, G.Evans, D.R.

(2019) Febs J. 286: 1204-1213

  • DOI: 10.1111/febs.14758
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dihydroorotase (DHOase) is involved in the de novo synthesis of pyrimidine in virtually all organisms, and it is usually associated with two other enzymes found in this biosynthetic pathway, carbamylphosphate synthetase and/or aspartate transcarbamyl ...

    Dihydroorotase (DHOase) is involved in the de novo synthesis of pyrimidine in virtually all organisms, and it is usually associated with two other enzymes found in this biosynthetic pathway, carbamylphosphate synthetase and/or aspartate transcarbamylase (ATCase). In the hyperthermophilic bacterium Aquifex aeolicus, ATCase and DHOase are noncovalently associated. Upon dissociation, ATCase keeps its activity entirely while DHOase is totally inactivated. It was previously shown that high pressure fully restores the activity of this isolated DHOase. On the basis of kinetic studies, site-directed mutagenesis and the use of peptides mimicking loop A, a loop that appears to block access to the active site, was proposed that this pressure-induced reactivation was due to the decrease in the volume of the system, -ΔV, resulting from the disruption of known ionic interactions between the loop and the main part of the protein. In this study, this interpretation is more precisely demonstrated by the determination of the crystallographic structure of isolated DHOase under pressure. In addition to the loop displacements, pressure induces a discrete rearrangement of the catalytic site aspartate 305, an effect that might additionally contribute to the reactivation of this enzyme.


    Related Citations: 
    • Activation of latent dihydroorotase from aquifex aeolicus by pressure
      Herve, G.,Guy-Evans, H.,Fernado, R.,Patel, C.,Hachem, F.,Evans, D.R.
      (2017) J. Biol. Chem. 292: 629


    Organizational Affiliation

    Laboratoire de Cristallographie & RMN biologiques (UMR 8015 CNRS), Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotase
A
423Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: pyrC
EC: 3.5.2.3
Find proteins for O66990 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66990
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.840α = 90.00
b = 176.488β = 90.00
c = 65.518γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
BUCCANEERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-03-27
    Type: Data collection, Database references