6BVE

Triosephosphate isomerase of Synechocystis in complex with 2-Phosphoglycolic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic BacteriaSynechocystis.

Castro-Torres, E.Jimenez-Sandoval, P.Fernandez-de Gortari, E.Lopez-Castillo, M.Baruch-Torres, N.Lopez-Hidalgo, M.Peralta-Castro, A.Diaz-Quezada, C.Sotelo-Mundo, R.R.Benitez-Cardoza, C.G.Espinoza-Fonseca, L.M.Ochoa-Leyva, A.Brieba, L.G.

(2018) Front Mol Biosci 5: 103-103

  • DOI: 10.3389/fmolb.2018.00103
  • Primary Citation of Related Structures:  
    6BVE

  • PubMed Abstract: 
  • In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insi ...

    In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria Synechocystis (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α) 8 fold. We found that oxidizing agents diamide (DA) and H 2 O 2 , as well as thiol-conjugating agents such as oxidized glutathione (GSSG) and methyl methanethiosulfonate (MMTS), do not inhibit the catalytic activity of SyTPI at concentrations required to inactivate plastidic and cytosolic TPIs from the plant model Arabidopsis thaliana (AtpdTPI and AtcTPI, respectively). The crystal structure of SyTPI revealed that each monomer contains three cysteines, C47, C127, and C176; however only the thiol group of C176 is solvent exposed. While AtcTPI and AtpdTPI are redox-regulated by chemical modifications of their accessible and reactive cysteines, we found that C176 of SyTPI is not sensitive to redox modification in vitro . Our data let us postulate that SyTPI was replaced by a eukaryotic TPI, because the latter contains redox-sensitive cysteines that may be subject to post-translational modifications required for modulating TPI's enzymatic activity.


    Organizational Affiliation

    Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Triosephosphate isomerase AB245Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: tpiAtpislr0783
EC: 5.3.1.1
Find proteins for Q59994 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q59994 
Go to UniProtKB:  Q59994
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download Ideal Coordinates CCD File 
A, B
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.88α = 90
b = 73.099β = 90
c = 85.175γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoFronteras de la Ciencia 13

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-15
    Changes: Author supporting evidence