1ML4

The PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Aspartate Transcarbamylase from the Hyperthermophilic Archaeon Pyrococcus abyssi: Thermostability and 1.8A Resolution Crystal Structure of the Catalytic Subunit Complexed With the Bisubstrate Analogue N-Phosphonacetyl-L-aspartate.

Van Boxstael, S.Cunin, R.Khan, S.Maes, D.

(2003) J.Mol.Biol. 326: 203-216


  • PubMed Abstract: 
  • The Pyrococcus abyssi aspartate transcarbamylase (ATCase) shows a high degree of structural conservation with respect to the well-studied mesophilic Escherichia coli ATCase, including the association of catalytic and regulatory subunits. The adaptati ...

    The Pyrococcus abyssi aspartate transcarbamylase (ATCase) shows a high degree of structural conservation with respect to the well-studied mesophilic Escherichia coli ATCase, including the association of catalytic and regulatory subunits. The adaptation of its catalytic function to high temperature was investigated, using enzyme purified from recombinant E.coli cells. At 90 degrees C, the activity of the trimeric catalytic subunit was shown to be intrinsically thermostable. Significant extrinsic stabilization by phosphate, a product of the reaction, was observed when the temperature was raised to 98 degrees C. Comparison with the holoenzyme showed that association with regulatory subunits further increases thermostability. To provide further insight into the mechanisms of its adaptation to high temperature, the crystal structure of the catalytic subunit liganded with the analogue N-phosphonacetyl-L-aspartate (PALA) was solved to 1.8A resolution and compared to that of the PALA-liganded catalytic subunit from E.coli. Interactions with PALA are strictly conserved. This, together with the similar activation energies calculated for the two proteins, suggests that the reaction mechanism of the P.abyssi catalytic subunit is similar to that of the E.coli subunit. Several structural elements potentially contributing to thermostability were identified: (i) a marked decrease in the number of thermolabile residues; (ii) an increased number of charged residues and a concomitant increase of salt links at the interface between the monomers, as well as the formation of an ion-pair network at the protein surface; (iii) the shortening of three loops and the shortening of the N and C termini. Other known thermostabilizing devices such as increased packing density or reduction of cavity volumes do not appear to contribute to the high thermostability of the P.abyssi enzyme.


    Organizational Affiliation

    Laboratorium voor Erfelijkheidsleer en Microbiologie, Faculteit der Wetenschappen, Vrije Universiteit Brussel (VUB), 1 E. Gryson ave, B-1070, Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate Transcarbamoylase
A
308Pyrococcus abyssi (strain GE5 / Orsay)Gene Names: pyrB
EC: 2.1.3.2
Find proteins for P77918 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P77918
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAL
Query on PAL

Download SDF File 
Download CCD File 
A
N-(PHOSPHONACETYL)-L-ASPARTIC ACID
C6 H10 N O8 P
ZZKNRXZVGOYGJT-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.172 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 81.095α = 90.00
b = 81.095β = 90.00
c = 141.959γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance