2VJY

Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.5 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: 10.1074/jbc.M806228200
  • Primary Citation of Related Structures:  
    2VJY, 2VK1, 2VK8

  • 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 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
MoleculeChainsSequence LengthOrganismDetailsImage
PYRUVATE DECARBOXYLASEA, B, C, D563Kluyveromyces lactisMutation(s): 0 
EC: 4.1.1.1
UniProt
Find proteins for Q12629 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore Q12629 
Go to UniProtKB:  Q12629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
ALK
Query on ALK

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D]
methoxy-[(1~{R})-1-oxidanylethyl]phosphinic acid
C3 H9 O4 P
BAMHLGPGGHPFTF-GSVOUGTGSA-N
 Ligand Interaction
ALU
Query on ALU

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C]
METHYL HYDROGEN (S)-ACETYLPHOSPHONATE
C3 H7 O4 P
QECABVMKPMRCRZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.76α = 90
b = 135.77β = 103.88
c = 107.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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 2.0: 2018-10-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 2.2: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 2.3: 2019-07-10
    Changes: Data collection, Derived calculations
  • Version 2.4: 2019-07-24
    Changes: Data collection
  • Version 2.5: 2019-10-16
    Changes: Data collection, Other