1RP0

Crystal Structure of Thi1 protein from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

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
  • Primary Citation of Related Structures:  
    1RP0

  • 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-hydroxymethylpyrimidine pyrophosphate (pyrimidine moiety) and another for the synthesis of 4-methyl-5-(beta-hydroxyethyl) thiazole phosphate (thiazole moiety) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiazole biosynthetic enzymeA, B284Arabidopsis thalianaMutation(s): 0 
Gene Names: THI1THI4At5g54770MBG8.3ARA6
EC: 2.4.2.60
Find proteins for Q38814 (Arabidopsis thaliana)
Explore Q38814 
Go to UniProtKB:  Q38814
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHZ
Query on AHZ

Download Ideal Coordinates CCD File 
D [auth A], G [auth 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 Ideal Coordinates CCD File 
E [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.356α = 90
b = 133.147β = 90
c = 142.301γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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