1PYD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1021/bi00075a008
  • Primary Citation of Related Structures:  
    1PYD

  • 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 interactions within each dimer but more limited ones between dimers ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASEA, B556Saccharomyces 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06169
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
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: 2.40 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.95α = 90
b = 74.67β = 116.39
c = 119.95γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-04-30
    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
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary