3RM5 | pdb_00003rm5

Structure of Trifunctional THI20 from Yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 
    0.279 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Models: experimental
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This is version 1.3 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: https://doi.org/10.1107/S0907444911024814
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 122.71 kDa 
  • Atom Count: 7,866 
  • Modeled Residue Count: 1,040 
  • Deposited Residue Count: 1,100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20
A, B
550Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: O1239THI20Thi20pYOL055C
EC: 2.7.1.49 (PDB Primary Data), 2.7.4.7 (PDB Primary Data), 3.5.99.2 (UniProt)
UniProt
Find proteins for Q08224 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08224 
Go to UniProtKB:  Q08224
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08224
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.279 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description