3RRW

Crystal structure of the TL29 protein from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the TL29 protein from Arabidopsis thaliana: An APX homolog without peroxidase activity.

Lundberg, E.Storm, P.Schroder, W.P.Funk, C.

(2011) J.Struct.Biol. 176: 24-31

  • DOI: 10.1016/j.jsb.2011.07.004

  • PubMed Abstract: 
  • TL29 is a plant-specific protein found in the thylakoid lumen of chloroplasts. Despite the putative requirement in plants for a peroxidase close to the site of photosynthetic oxygen production, and the sequence homology of TL29 to ascorbate peroxidas ...

    TL29 is a plant-specific protein found in the thylakoid lumen of chloroplasts. Despite the putative requirement in plants for a peroxidase close to the site of photosynthetic oxygen production, and the sequence homology of TL29 to ascorbate peroxidases, so far biochemical methods have not shown this enzyme to possess peroxidase activity. Here we report the three-dimensional X-ray crystal structure of recombinant TL29 from Arabidopsis thaliana at a resolution of 2.5Å. The overall structure of TL29 is mainly alpha helical with six longer and six shorter helical segments. The TL29 structure resembles that of typical ascorbate peroxidases, however, crucial differences were found in regions that would be important for heme and ascorbate binding. Such differences suggest it to be highly unlikely that TL29 functions as a peroxidase.


    Organizational Affiliation

    Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thylakoid lumenal 29 kDa protein, chloroplastic
A, B
268Arabidopsis thalianaMutation(s): 0 
Gene Names: TL29 (APX4)
EC: 1.-.-.-
Find proteins for P82281 (Arabidopsis thaliana)
Go to UniProtKB:  P82281
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.350α = 90.00
b = 92.350β = 90.00
c = 143.460γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
PHENIXmodel building
PHENIXphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-08-17
    Type: Database references
  • Version 1.2: 2011-09-21
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Data collection, Refinement description