Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 58.22 kDa 
• Atom Count: 4724 
• Modelled Residue Count: 525 
• Deposited Residue Count: 536 
• Unique protein chains: 1

4JD5

Crystal Structure of Benzoylformate Decarboxylase Mutant L403E

• PDB DOI: 10.2210/pdb4JD5/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-02-23 Released: 2013-05-22 
• Deposition Author(s): Novak, W.R.P., Andrews, F.H., Tom, A.R., Gunderman, P.R., McLeish, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.152 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 

Literature

A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.

Andrews, F.H., Tom, A.R., Gunderman, P.R., Novak, W.R., McLeish, M.J.

(2013) Biochemistry 52: 3028-3030

• PubMed: 23607689 
• DOI: 10.1021/bi400368j
• Primary Citation of Related Structures:  
  4GG1, 4GM0, 4GM1, 4GM4, 4GP9, 4GPE, 4JD5


• PubMed Abstract: 
  

It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of a bulky hydrophobic residue located directly below the cofactor. Here we report the use of site-saturation mutagenesis to generate variants of this residue (Leu403) in benzoylformate decarboxylase. The observed 3 orders of magnitude range in k(cat)/K(m) values suggested that conformational changes in the cofactor could be influencing catalysis. However, X-ray structures of several variants were determined, and there was remarkably little change in ThDP conformation. Rather, it seemed that, once the V-conformation was attained, residue size and hydrophobicity were more important for enzyme activity.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A	536	Pseudomonas putida	Mutation(s): 1  Gene Names: mdlC EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida) Explore P20906  Go to UniProtKB:  P20906

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TZD	B [auth A]	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE C12 H18 N4 O8 P2 S ZGJUYGIRPQSCFA-UHFFFAOYSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.152 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.55	α = 90
b = 95.79	β = 90
c = 137.15	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-23 
• Released Date: 2013-05-22 
Deposition Author(s): Novak, W.R.P., Andrews, F.H., Tom, A.R., Gunderman, P.R., McLeish, M.J.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release