Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 67491.23 
• Atom Count: 4726 
• Residue Count: 639 
• Unique protein chains: 1

1EUN

STRUCTURE OF 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE FROM ESCHERICHIA COLI

• DOI: 10.2210/pdb1EUN/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)


• Deposited: 2000-04-17 Released: 2001-02-07 
• Deposition Author(s): Allard, J., Grochulski, P., Sygusch, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.259 
• R-Value Work: 0.202 

Literature

Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution.

Allard, J., Grochulski, P., Sygusch, J.

(2001) Proc.Natl.Acad.Sci.USA 98: 3679-3684

• PubMed: 11274385 
• DOI: 10.1073/pnas.071380898
• Primary Citation of Related Structures:  
  1EUA


• PubMed Abstract: 
  

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. The enzyme is a class I aldolase whose reaction mechanism involves formation of Schiff base intermediates between Lys-133 and a keto substrate. A covalent adduct was trapped by flash freezing KDPG aldolase crystals soaked with 10 mM pyruvate in acidic conditions at pH 4.6. Structure determination to 1.95-A resolution showed that pyruvate had undergone nucleophilic attack with Lys-133, forming a protonated carbinolamine intermediate, a functional Schiff base precursor, which was stabilized by hydrogen bonding with active site residues. Carbinolamine interaction with Glu-45 indicates general base catalysis of several rate steps. Stereospecific addition is ensured by aromatic interaction of Phe-135 with the pyruvate methyl group. In the native structure, Lys-133 donates all of its hydrogen bonds, indicating the presence of an epsilon-ammonium salt group. Nucleophilic activation is postulated to occur by proton transfer in the monoprotonated zwitterionic pair (Glu-45/Lys-133). Formation of the zwitterionic pair requires prior side chain rearrangement by protonated Lys-133 to displace a water molecule, hydrogen bonded to the zwitterionic residues.

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Organizational Affiliation: 

Département de Biochimie, Université de Montréal, Montreal, QC, H3C 3J7 Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
KDPG ALDOLASE	A, B, C	213	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: eda (hga, kdgA)
Find proteins for P0A955 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A955

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.259 
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 54.950	α = 90.00
b = 85.210	β = 90.00
c = 133.690	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-04-17 
• Released Date: 2001-02-07 
• Deposition Author(s): Allard, J., Grochulski, P., Sygusch, J.

Revision History 

• Version 1.0: 2001-02-07
  Type: Initial release
• Version 1.1: 2008-04-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance