4FEG

High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin.

Meyer, D.Neumann, P.Koers, E.Sjuts, H.Ludtke, S.Sheldrick, G.M.Ficner, R.Tittmann, K.

(2012) Proc.Natl.Acad.Sci.USA 109: 10867-10872

  • DOI: 10.1073/pnas.1201280109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enami ...

    Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 Å resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than π-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms.


    Organizational Affiliation

    Albrecht-von-Haller Institute and Göttingen Center for Molecular Biosciences, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate oxidase
A, B
603N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PYR
Query on PYR

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A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TDM
Query on TDM

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A, B
2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE
2-HYDROXYETHYLTHIAMIN DIPHOSPHATE
C14 H22 N4 O8 P2 S
ZZLCKFKIIVXBQU-NTEUORMPSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.119 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.600α = 90.00
b = 154.400β = 90.00
c = 165.520γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SHELXrefinement
XSCALEdata scaling
PHENIXphasing
SHELXL-97refinement
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-11
    Type: Database references
  • Version 1.2: 2012-07-25
    Type: Database references