Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 158.27 kDa 
• Atom Count: 11271 
• Modelled Residue Count: 1434 
• Deposited Residue Count: 1464 
• Unique protein chains: 1

1JPM

L-Ala-D/L-Glu Epimerase

• DOI: 10.2210/pdb1JPM/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-08-02 Released: 2001-12-21 
• Deposition Author(s): Gulick, A.M., Schmidt, D.M.Z., Gerlt, J.A., Rayment, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis.

Gulick, A.M., Schmidt, D.M., Gerlt, J.A., Rayment, I.

(2001) Biochemistry 40: 15716-15724

• PubMed: 11747448 
• DOI: 10.1021/bi011641p
• Primary Citation of Related Structures:  
  1JPM, 1JPD


• PubMed Abstract: 
  

The members of the enolase superfamily catalyze different overall reactions, yet share a partial reaction that involves Mg(2+)-assisted enolization of the substrate carboxylate anion. The fate of the resulting enolate intermediate is determined by the active site of each enzyme. Several members of this superfamily have been structurally characterized to permit an understanding of the evolutionary strategy for using a common structural motif to catalyze different overall reactions. In the preceding paper, two new members of the superfamily were identified that catalyze the epimerization of the glutamate residue in L-Ala-D/L-Glu. These enzymes belong to the muconate lactonizing enzyme subgroup of the enolase superfamily, and their sequences are only 31% identical. The structure of YcjG, the epimerase from Escherichia coli, was determined by MAD phasing using both the SeMet-labeled protein and a heavy atom derivative. The structure of YkfB, the epimerase from Bacillus subtilis, was determined by molecular replacement using the muconate lactonizing enzyme as a search model. In this paper, we report the three-dimensional structures of these enzymes and compare them to the structure of o-succinylbenzoate synthase, another member of the muconate lactonizing enzyme subgroup.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-Ala-D/L-Glu Epimerase	A, B, C, D	366	Bacillus subtilis	Mutation(s): 0  Gene Names: ykfB EC: 5.1.1.20
Find proteins for O34508 (Bacillus subtilis (strain 168)) Explore O34508  Go to UniProtKB:  O34508

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.63	α = 90
b = 157.63	β = 90
c = 168.32	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-02 
• Released Date: 2001-12-21 
Deposition Author(s): Gulick, A.M., Schmidt, D.M.Z., Gerlt, J.A., Rayment, I.

Revision History  

• Version 1.0: 2001-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance