Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 135.28 kDa 
• Atom Count: 10254 
• Residue Count: 1170 
• Unique protein chains: 1

2EZ9

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate

• DOI: 10.2210/pdb2EZ9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-10 Released: 2006-04-25 
• Deposition Author(s): Wille, G., Meyer, D., Steinmetz, A., Hinze, E., Golbik, R., Tittmann, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography.

Wille, G., Meyer, D., Steinmetz, A., Hinze, E., Golbik, R., Tittmann, K.

(2006) Nat Chem Biol 2: 324-328

• PubMed: 16680160 
• DOI: 10.1038/nchembio788
• Primary Citation of Related Structures:  
  2EZ9, 2EZ8, 2EZ4, 2EZU, 2EZT


• PubMed Abstract: 
  

Enzymes that use the cofactor thiamin diphosphate (ThDP, 1), the biologically active form of vitamin B(1), are involved in numerous metabolic pathways in all organisms. Although a theory of the cofactor's underlying reaction mechanism has been established over the last five decades, the three-dimensional structures of most major reaction intermediates of ThDP enzymes have remained elusive. Here, we report the X-ray structures of key intermediates in the oxidative decarboxylation of pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP- and flavin-dependent enzyme pyruvate oxidase (POX)3 from Lactobacillus plantarum. The structures of 2-lactyl-ThDP (LThDP, 2) and its stable phosphonate analog, of 2-hydroxyethyl-ThDP (HEThDP, 3) enamine and of 2-acetyl-ThDP (AcThDP, 4; all shown bound to the enzyme's active site) provide profound insights into the chemical mechanisms and the stereochemical course of thiamin catalysis. These snapshots also suggest a mechanism for a phosphate-linked acyl transfer coupled to electron transfer in a radical reaction of pyruvate oxidase.

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Organizational Affiliation: 

Institut für Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle/Saale, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate oxidase	A, B	603	Lactiplantibacillus plantarum	Mutation(s): 1  Gene Names: pox5 EC: 1.2.3.3
Find proteins for P37063 (Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore P37063  Go to UniProtKB:  P37063

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TDK	A, B	3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM C15 H26 N4 O11 P3 S ILGXNMPRCMTAOK-HNNXBMFYSA-O
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.661	α = 90
b = 154.517	β = 90
c = 165.64	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-11-10 
• Released Date: 2006-04-25 
Deposition Author(s): Wille, G., Meyer, D., Steinmetz, A., Hinze, E., Golbik, R., Tittmann, K.

Revision History 

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description