1PVD

CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution.

Arjunan, P.Umland, T.Dyda, F.Swaminathan, S.Furey, W.Sax, M.Farrenkopf, B.Gao, Y.Zhang, D.Jordan, F.

(1996) J Mol Biol 256: 590-600

  • DOI: 10.1006/jmbi.1996.0111
  • Primary Citation of Related Structures:  
    1PVD

  • PubMed Abstract: 
  • The crystal structure of pyruvate decarboxylase (EC 4.1.1.1), a thiamin diphosphate-dependent enzyme isolated from Saccharomyces cerevisiae, has been determined and refined to a resolution of 2.3 A. Pyruvate decarboxylase is a homotetrameric enzyme which crystallizes with two subunits in an asymmetric unit ...

    The crystal structure of pyruvate decarboxylase (EC 4.1.1.1), a thiamin diphosphate-dependent enzyme isolated from Saccharomyces cerevisiae, has been determined and refined to a resolution of 2.3 A. Pyruvate decarboxylase is a homotetrameric enzyme which crystallizes with two subunits in an asymmetric unit. The structure has been refined by a combination of simulated annealing and restrained least squares to an R factor of 0.165 for 46,787 reflections. As in the corresponding enzyme from Saccharomyces uvarum, the homotetrameric holoenzyme assembly has approximate 222 symmetry. In addition to providing more accurate atomic parameters and certainty in the sequence assignments, the high resolution and extensive refinement resulted in the identification of several tightly bound water molecules in key structural positions. These water molecules have low temperature factors and make several hydrogen bonds with protein residues. There are six such water molecules in each cofactor binding site, and one of them is involved in coordination with the required magnesium ion. Another may be involved in the catalytic reaction mechanism. The refined model includes 1074 amino acid residues (two subunits), two thiamin diphosphate cofactors, two magnesium ions associated with cofactor binding and 440 water molecules. From the refined model we conclude that the resting state of the enzyme-cofactor complex is such that the cofactor is already deprotonated at the N4' position of the pyrimidine ring, and is poised to accept a proton from the C2 position of the thiazolium ring.


    Related Citations: 
    • Multiple Crystal Forms of Brewers' Yeast Pyruvate Decarboxylase: Characterization and Preliminary Crystallographic Analysis
      Dyda, F., Furey, W., Swaminathan, S., Sax, M., Farrenkopf, B., Jordan, F.
      (1991) Biochemistry And Physiology Of Thiamin Diphosphate Enzymes --: 115
    • Structure and Expression of Yeast Pyruvate Decarboxylase Structural Genes
      Hohmann, S.
      (1991) Biochemistry And Physiology Of Thiamin Diphosphate Enzymes --: 106
    • Preliminary Crystallographic Data for the Thiamin Diphosphate-Dependent Enzyme Pyruvate Decarboxylase from Brewers' Yeast
      Dyda, F., Furey, W., Swaminathan, S., Sax, M., Farrenkopf, B., Jordan, F.
      (1990) J Biol Chem 265: 17413

    Organizational Affiliation

    Biocrystallography Laboratory, VA Medical Center, Pittsburgh, PA 15240, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASEA, B555Saccharomyces cerevisiaeMutation(s): 0 
EC: 4.1.1.1 (PDB Primary Data), 4.1.1 (UniProt), 4.1.1.43 (UniProt), 4.1.1.72 (UniProt), 4.1.1.74 (UniProt)
UniProt
Find proteins for P06169 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06169 
Go to UniProtKB:  P06169
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.06α = 90
b = 74.75β = 116.58
c = 120.32γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 1995-04-20 
  • Released Date: 1995-07-31 
  • Deposition Author(s): Furey, W., Arjunan, P.

Revision History  (Full details and data files)

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description