1QPB

PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study

Lu, G.Dobritzsch, D.Baumann, S.Schneider, G.Konig, S.

(2000) Eur J Biochem 267: 861

  • DOI: https://doi.org/10.1046/j.1432-1327.2000.01070.x
  • Primary Citation of Related Structures:  
    1QPB

  • PubMed Abstract: 

    The crystal structure of the complex of the thiamine diphosphate dependent tetrameric enzyme pyruvate decarboxylase (PDC) from brewer's yeast strain with the activator pyruvamide has been determined to 2.4 A resolution. The asymmetric unit of the crystal contains two subunits, and the tetrameric molecule is generated by crystallographic symmetry. Structure analysis revealed conformational nonequivalence of the active sites. One of the two active sites in the asymmetric unit was found in an open conformation, with two active site loop regions (residues 104-113 and 290-304) disordered. In the other subunit, these loop regions are well-ordered and shield the active site from the bulk solution. In the closed enzyme subunit, one molecule of pyruvamide is bound in the active site channel, and is located in the vicinity of the thiazolium ring of the cofactor. A second pyruvamide binding site was found at the interface between the Pyr and the R domains of the subunit in the closed conformation, about 10 A away from residue C221. This second pyruvamide molecule might function in stabilizing the unique orientation of the R domain in this subunit which in turn is important for dimer-dimer interactions in the activated tetramer. No difference electron density in the close vicinity of the side chain of residue C221 was found, indicating that this residue does not form a covalent adduct with an activator molecule. Kinetic experiments showed that substrate activation was not affected by oxidation of cysteine residues and therefore does not seem to be dependent on intact thiol groups in the enzyme. The results suggest that a disorder-order transition of two active-site loop regions is a key event in the activation process triggered by the activator pyruvamide and that covalent modification of C221 is not required for this transition to occur. Based on these findings, a possible mechanism for the activation of PDC by its substrate, pyruvate, is proposed.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASE (FORM B)
A, B
563Saccharomyces pastorianus Weihenstephan 34/70Mutation(s): 4 
EC: 4.1.1.1 (PDB Primary Data), 4.1.1.74 (UniProt), 4.1.1.72 (UniProt), 4.1.1.43 (UniProt), 4.1.1 (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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PYM PDBBind:  1QPB Kd: 4.40e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.049α = 90
b = 119.7β = 120.21
c = 81.283γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description