1PYD

CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution.

Dyda, F.Furey, W.Swaminathan, S.Sax, M.Farrenkopf, B.Jordan, F.

(1993) Biochemistry 32: 6165-6170


  • PubMed Abstract: 
  • The crystal structure of brewers' yeast pyruvate decarboxylase, a thiamin diphosphate dependent alpha-keto acid decarboxylase, has been determined to 2.4-A resolution. The homotetrameric assembly contains two dimers, exhibiting strong intermonomer in ...

    The crystal structure of brewers' yeast pyruvate decarboxylase, a thiamin diphosphate dependent alpha-keto acid decarboxylase, has been determined to 2.4-A resolution. The homotetrameric assembly contains two dimers, exhibiting strong intermonomer interactions within each dimer but more limited ones between dimers. Each monomeric subunit is partitioned into three structural domains, all folding according to a mixed alpha/beta motif. Two of these domains are associated with cofactor binding, while the other is associated with substrate activation. The catalytic centers containing both thiamin diphosphate and Mg(II) are located deep in the intermonomer interface within each dimer. Amino acids important in cofactor binding and likely to participate in catalysis and substrate activation are identified.


    Related Citations: 
    • Multiple Crystal Forms of Brewers' Yeast Pyruvate Decarboxylase: Characterization and Preliminary Crystallographic Analysis
      Dyda, F.,Furey, W.,Swaminathan, S.,Sax, M.,Jordan, F.,Farrenkopf, B.
      (1991) Biochemistry and Physiology of Thiamin Diphosphate Enzymes --: 115
    • 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, Veterans Administration Medical Center, Pittsburgh, Pennsylvania 15240.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE DECARBOXYLASE
A, B
556Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PDC1
EC: 4.1.1.-, 4.1.1.43, 4.1.1.72, 4.1.1.74
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
TDP
Query on TDP

Download SDF File 
Download CCD File 
A, B
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 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: 2.4 Å
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.950α = 90.00
b = 74.670β = 116.39
c = 119.950γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-03-23 
  • Released Date: 1994-04-30 
  • Deposition Author(s): Furey, W., Dyda, F.

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance