1IG0

Crystal Structure of yeast Thiamin Pyrophosphokinase

• PDB DOI: https://doi.org/10.2210/pdb1IG0/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-04-16 Released: 2001-06-20 
• Deposition Author(s): Baker, L.-J., Dorocke, J.A., Harris, R.A., Timm, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

The crystal structure of yeast thiamin pyrophosphokinase.

Baker, L.J., Dorocke, J.A., Harris, R.A., Timm, D.E.

(2001) Structure 9: 539-546

• PubMed: 11435118 
• DOI: https://doi.org/10.1016/s0969-2126(01)00615-3
• Primary Citation of Related Structures:  
  1IG0


• PubMed Abstract: 
  

  Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. TPK has no sequence homologs in the PDB and functions by an unknown mechanism. The TPK structure has been determined as a significant step toward elucidating its catalytic action.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 73.85 kDa 
• Atom Count: 5,830 
• Modelled Residue Count: 636 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamin pyrophosphokinase	A, B	319	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: THI80 EC: 2.7.6.2
UniProt
Find proteins for P35202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35202  Go to UniProtKB:  P35202

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIB	C [auth A], D [auth B]	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM C12 H17 N4 O S JZRWCGZRTZMZEH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.313	α = 90
b = 130.839	β = 90
c = 44.319	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-20 
Deposition Author(s): Baker, L.-J., Dorocke, J.A., Harris, R.A., Timm, D.E.

Revision History  

• Version 1.0: 2001-06-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Structure summary