Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 61.63 kDa 
• Atom Count: 4688 
• Modelled Residue Count: 556 
• Deposited Residue Count: 568 
• Unique protein chains: 1

1RP0

Crystal Structure of Thi1 protein from Arabidopsis thaliana

• PDB DOI: 10.2210/pdb1RP0/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-12-02 Released: 2005-02-22 
• Deposition Author(s): Godoi, P.H.C., Van Sluys, M.A., Menck, C.F.M., Oliva, G.

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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 

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

• PubMed: 16912043 
• 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). 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiazole biosynthetic enzyme	A, B	284	Arabidopsis thaliana	Mutation(s): 0  Gene Names: THI1, THI4, At5g54770, MBG8.3, ARA6 EC: 2.4.2.60
UniProt
Find proteins for Q38814 (Arabidopsis thaliana) Explore Q38814  Go to UniProtKB:  Q38814

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHZ	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
HTO	E [auth A]	HEPTANE-1,2,3-TRIOL C7 H16 O3 HXYCHJFUBNTKQR-RNFRBKRXSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 102.356	α = 90
b = 133.147	β = 90
c = 142.301	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-02 
• Released Date: 2005-02-22 
Deposition Author(s): Godoi, P.H.C., Van Sluys, M.A., Menck, C.F.M., Oliva, G.

Revision History  

• 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