1UJP

Crystal Structure of Tryptophan Synthase A-Subunit From Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry.

Asada, Y.Sawano, M.Ogasahara, K.Nakamura, J.Ota, M.Kuroishi, C.Sugahara, M.Yutani, K.Kunishima, N.

(2005) J.Biochem.(Tokyo) 138: 343-353

  • DOI: 10.1093/jb/mvi133

  • PubMed Abstract: 
  • In order to elucidate the thermo-stabilization mechanism of the tryptophan synthase alpha-subunit from the extreme thermophile Thermus thermophilus HB8 (Tt-alpha-subunit), its crystal structure was determined and its stability was examined using DSC. ...

    In order to elucidate the thermo-stabilization mechanism of the tryptophan synthase alpha-subunit from the extreme thermophile Thermus thermophilus HB8 (Tt-alpha-subunit), its crystal structure was determined and its stability was examined using DSC. The results were compared to those of other orthologs from mesophilic and hyperthermophilic organisms. The denaturation temperature of the Tt-alpha-subunit was higher than that of the alpha-subunit from S. typhimurium (St-alpha-subunit) but lower than that of the alpha-subunit from P. furiosus (Pf-alpha-subunit). Specific denaturation enthalpy and specific denaturation heat capacity values of the Tt-alpha-subunit were the lowest among the three proteins, suggesting that entropy effects are responsible for the stabilization of the Tt-alpha-subunit. Based on a structural comparison with the St-alpha-subunit, two deletions in loop regions, an increase in the number of ion pairs and a decrease in cavity volume seem to be responsible for the stabilization of the Tt-alpha-subunit. The results of structural comparison suggest that the native structure of the Tt-alpha-subunit is better adapted to an ideally stable structure than that of the St-alpha-subunit, but worse than that of the Pf-alpha-subunit. The results of calorimetry suggest that the residual structure of the Tt-alpha-subunit in the denatured state contributes to the stabilization.


    Organizational Affiliation

    Advanced Protein Crystallography Research Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase alpha chain
A
271Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
Find proteins for P16608 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P16608
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.400α = 90.00
b = 76.868β = 115.08
c = 42.774γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance