4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Observation of a stable carbene at the active site of a thiamin enzyme.

Meyer, D., Neumann, P., Ficner, R., Tittmann, K.

(2013) Nat Chem Biol 9: 488-490

  • DOI: 10.1038/nchembio.1275
  • Primary Citation of Related Structures:  
    4KGD

  • PubMed Abstract: 

    • Carbenes are highly reactive chemical compounds that are exploited as ligands in organometallic chemistry and are powerful organic catalysts. They were postulated to occur as transient intermediates in enzymes, yet their existence in a biological system could never be demonstrated directly ...

    Carbenes are highly reactive chemical compounds that are exploited as ligands in organometallic chemistry and are powerful organic catalysts. They were postulated to occur as transient intermediates in enzymes, yet their existence in a biological system could never be demonstrated directly. We present spectroscopic and structural data of a thiamin enzyme in a noncovalent complex with substrate, which implicate accumulation of a stable carbene as a major resonance contributor to deprotonated thiamin.

    Organizational Affiliation: 

    Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Ernst-Caspari-Haus, Georg-August University Göttingen, Göttingen, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate oxidaseA, B603Lactobacillus plantarum JDM1Mutation(s): 0 
Gene Names: JDM1_2870, pox5
EC: 1.2.3.3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
 C [auth A], L [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
TDP
Query on TDP
Download Ideal Coordinates CCD File 
 F [auth A], N [auth B]THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 E [auth A], O [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , P [auth B] , Q [auth B] , R [auth B] , S [auth B] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
 K [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 D [auth A], M [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.127 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.28α = 90
b = 154.16β = 90
c = 165.47γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description