3RM5

Structure of Trifunctional THI20 from Yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of trifunctional THI20 from yeast.

French, J.B.Begley, T.P.Ealick, S.E.

(2011) Acta Crystallogr D Biol Crystallogr 67: 784-791

  • DOI: 10.1107/S0907444911024814
  • Primary Citation of Related Structures:  
    3RM5

  • PubMed Abstract: 
  • In a recently characterized thiamin-salvage pathway, thiamin-degradation products are hydrolyzed by thiaminase II, yielding 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). This compound is an intermediate in thiamin biosynthesis that, once phosphor ...

    In a recently characterized thiamin-salvage pathway, thiamin-degradation products are hydrolyzed by thiaminase II, yielding 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). This compound is an intermediate in thiamin biosynthesis that, once phosphorylated by an HMP kinase, can be used to synthesize thiamin monophosphate. Here, the crystal structure of Saccharomyces cerevisiae THI20, a trifunctional enzyme containing an N-terminal HMP kinase/HMP-P kinase (ThiD-like) domain and a C-terminal thiaminase II (TenA-like) domain, is presented. Comparison to structures of the monofunctional enzymes reveals that while the ThiD-like dimer observed in THI20 resembles other ThiD structures, the TenA-like domain, which is tetrameric in all previously reported structures, forms a dimer. Similarly, the active site of the ThiD-like domain of THI20 is highly similar to other known ThiD enzymes, while the TenA-like active site shows unique features compared with previously structurally characterized TenAs. In addition, a survey of known TenA structures revealed two structural classes, both of which have distinct conserved features. The TenA domain of THI20 possesses some features of both classes, consistent with its ability to hydrolyze both thiamin and the thiamin-degradation product 2-methyl-4-amino-5-aminomethylpyrimidine.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20AB550Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: O1239THI20Thi20pYOL055C
EC: 2.7.1.49 (PDB Primary Data), 2.7.4.7 (PDB Primary Data)
Find proteins for Q08224 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08224 
Go to UniProtKB:  Q08224
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.704α = 90
b = 140.096β = 90
c = 143.273γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Other
  • Version 1.2: 2017-11-08
    Changes: Refinement description