1RP0

Crystal Structure of Thi1 protein from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the thiazole biosynthetic enzyme THI1 from Arabidopsis thaliana.

Godoi, P.H.Galhardo, R.S.Luche, D.D.Van Sluys, M.A.Menck, C.F.Oliva, G.

(2006) J.Biol.Chem. 281: 30957-30966

  • DOI: 10.1074/jbc.M604469200

  • PubMed Abstract: 
  • Thiamin pyrophosphate is an essential coenzyme in all organisms that depend on fermentation, respiration or photosynthesis to produce ATP. It is synthesized through two independent biosynthetic routes: one for the synthesis of 2-methyl-4-amino-5-hydr ...

    Thiamin pyrophosphate is an essential coenzyme in all organisms that depend on fermentation, respiration or photosynthesis to produce ATP. It is synthesized through two independent biosynthetic routes: one for the synthesis of 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate (pyrimidine moiety) and another for the synthesis of 4-methyl-5-(beta-hydroxyethyl) thiazole phosphate (thiazole moiety). Herein, we will describe the three-dimensional structure of THI1 protein from Arabidopsis thaliana determined by single wavelength anomalous diffraction to 1.6A resolution. The protein was produced using heterologous expression in bacteria, unexpectedly bound to 2-carboxylate-4-methyl-5-beta-(ethyl adenosine 5-diphosphate) thiazole, a potential intermediate of the thiazole biosynthesis in Eukaryotes. THI1 has a topology similar to dinucleotide binding domains and although details concerning its function are unknown, this work provides new clues about the thiazole biosynthesis in Eukaryotes.


    Organizational Affiliation

    Departamento de Física e Informática, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, CP 369, 13560-970, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiazole biosynthetic enzyme
A, B
284Arabidopsis thalianaGene Names: THI1 (ARA6, THI4)
Find proteins for Q38814 (Arabidopsis thaliana)
Go to UniProtKB:  Q38814
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
ADENOSINE DIPHOSPHATE 5-(BETA-ETHYL)-4-METHYL-THIAZOLE-2-CARBOXYLIC ACID
C17 H19 N6 O12 P2 S
VGXBGQACJQRWLV-LKGUXBDMSA-K
 Ligand Interaction
HTO
Query on HTO

Download SDF File 
Download CCD File 
A
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.356α = 90.00
b = 133.147β = 90.00
c = 142.301γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOSFLMdata reduction
SOLVEphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance