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 (software)

Macromolecule Content

• Total Structure Weight: 56.63 kDa 
• Atom Count: 4462 
• Modelled Residue Count: 525 
• Deposited Residue Count: 525 
• Unique protein chains: 1

3F6E

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor 3-PKB

• DOI: 10.2210/pdb3F6E/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-05 Released: 2008-12-09 
• Deposition Author(s): Brandt, G.S., McLeish, M.J., Kenyon, G.L., Petsko, G.A., Ringe, D., Jordan, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.212 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.

Chakraborty, S., Nemeria, N.S., Balakrishnan, A., Brandt, G.S., Kneen, M.M., Yep, A., McLeish, M.J., Kenyon, G.L., Petsko, G.A., Ringe, D., Jordan, F.

(2009) Biochemistry 48: 981-994

• PubMed: 19140682 
• DOI: 10.1021/bi801810h
• Primary Citation of Related Structures:  
  3F6B, 3F6E


• PubMed Abstract: 
  

The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.

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Organizational Affiliation: 

Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	X	525	Pseudomonas putida	Mutation(s): 0  Gene Names: mdlC EC: 4.1.1.7
Find proteins for P20906 (Pseudomonas putida) Explore P20906  Go to UniProtKB:  P20906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8PA	X	3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium C20 H26 N5 O8 P2 S HUCLASQGRJZNFE-RTRPANQVSA-O
MG	X	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8PA	Kd :  4139999.75   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.212 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.09	α = 90
b = 95.807	β = 90
c = 137.324	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-05 
• Released Date: 2008-12-09 
Deposition Author(s): Brandt, G.S., McLeish, M.J., Kenyon, G.L., Petsko, G.A., Ringe, D., Jordan, F.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description