2VK1

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.

Kutter, S.Weiss, M.S.Wille, G.Golbik, R.Spinka, M.Konig, S.

(2009) J Biol Chem 284: 12136

  • DOI: https://doi.org/10.1074/jbc.M806228200

  • PubMed Abstract: 

    The mechanism by which the enzyme pyruvate decarboxylase from two yeast species is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants, or of enzyme complexes from two yeast species, three of them reported here for the first time, provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighboring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, one of which provides two histidine residues necessary to complete the enzymatically competent active site architecture. The structural data are complemented and supported by kinetic investigations and binding studies, providing a consistent picture of the structural changes occurring upon enzyme activation.


  • Organizational Affiliation

    Institute for Biochemistry and Biotechnology, Faculty of Biological Sciences, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASE ISOZYME 1
A, B, C, D
563Saccharomyces cerevisiaeMutation(s): 1 
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
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
Q [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
PYR
Query on PYR

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D]
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.88α = 90
b = 141.31β = 107.19
c = 114.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    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: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2023-12-13
    Changes: Refinement description