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: 2.3 Å
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 w ...

    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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE DECARBOXYLASE
A, B
555Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PDC1
EC: 4.1.1.1, 4.1.1.-
Find proteins for P06169 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06169
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.060α = 90.00
b = 74.750β = 116.58
c = 120.320γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
GPRLSArefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance