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 (software)

Macromolecule Content

• Total Structure Weight: 71.47 kDa 
• Atom Count: 5237 
• Modelled Residue Count: 618 
• Deposited Residue Count: 652 
• Unique protein chains: 1

3FPZ

Saccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase

• PDB DOI: 10.2210/pdb3FPZ/pdb
• Entry: 3FPZ supersedes: 2GJC

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-06 Released: 2010-01-19 
• Deposition Author(s): Bale, S., Chatterjee, A., Dorrestein, P.C., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase.

Chatterjee, A., Abeydeera, N.D., Bale, S., Pai, P.J., Dorrestein, P.C., Russell, D.H., Ealick, S.E., Begley, T.P.

(2011) Nature 478: 542-546

• PubMed: 22031445 
• DOI: 10.1038/nature10503
• Primary Citation of Related Structures:  
  3FPZ


• PubMed Abstract: 
  

Thiamine pyrophosphate 1 is an essential cofactor in all living systems. Its biosynthesis involves the separate syntheses of the pyrimidine 2 and thiazole 3 precursors, which are then coupled. Two biosynthetic routes to the thiamine thiazole have been identified. In prokaryotes, five enzymes act on three substrates to produce the thiazole via a complex oxidative condensation reaction, the mechanistic details of which are now well established. In contrast, only one gene product is involved in thiazole biosynthesis in eukaryotes (THI4p in Saccharomyces cerevisiae). Here we report the preparation of fully active recombinant wild-type THI4p, the identification of an iron-dependent sulphide transfer reaction from a conserved cysteine residue of the protein to a reaction intermediate and the demonstration that THI4p is a suicide enzyme undergoing only a single turnover.

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Related Citations: 

• Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae.
  Jurgenson, C.T., Chatterjee, A., Begley, T.P., Ealick, S.E.
  (2006) Biochemistry 45: 11061

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiazole biosynthetic enzyme	A, B	326	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: THI4, ESP35, MOL1, YGR144W, G6620 EC: 2.4.2.60
UniProt
Find proteins for P32318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32318  Go to UniProtKB:  P32318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHZ	C [auth A], F [auth B]	ADENOSINE DIPHOSPHATE 5-(BETA-ETHYL)-4-METHYL-THIAZOLE-2-CARBOXYLIC ACID C17 H19 N6 O12 P2 S VGXBGQACJQRWLV-LKGUXBDMSA-K
SO4	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA	A, B	PEPTIDE LINKING	C3 H5 N O2		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.696	α = 90
b = 140.696	β = 90
c = 73.325	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-06 
• Released Date: 2010-01-19 
Deposition Author(s): Bale, S., Chatterjee, A., Dorrestein, P.C., Begley, T.P., Ealick, S.E.
• This entry supersedes: 2GJC

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-09
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description