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Glycolysis: Preparatory Phase

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In cellular metabolism (the complete breakdown of glucose to extract energy), glycolysis is the first step. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport, where the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These...

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This lesson deals with the crossed aldol reaction using weak bases. The self-condensation of an aldehyde having α hydrogen is prevented by adding it slowly to a mixture of formaldehyde and weak bases like hydroxide and alkoxide. Upon slow addition of the aldehyde, the base deprotonates the α carbon of the aldehyde to form the corresponding enolate. The enolate subsequently attacks the formaldehyde to form a single crossed product. Figure 1 depicts the aforementioned reaction.

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

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

J Allard¹, P Grochulski, J Sygusch

¹Département de Biochimie, Université de Montréal, Montreal, QC, H3C 3J7 Canada.

Proceedings of the National Academy of Sciences of the United States of America

|March 29, 2001

Summary

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase

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Area of Science:

Biochemistry
Enzymology
Structural Biology

Background:

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase is a class I aldolase.
Its mechanism involves Schiff base intermediates with Lys-133.
KDPG aldolase catalyzes the reversible cleavage of KDPG into pyruvate and glyceraldehyde-3-phosphate.

Purpose of the Study:

To elucidate the reaction mechanism of KDPG aldolase.
To determine the structure of a covalent adduct formed by KDPG aldolase and pyruvate.
To understand the role of active site residues in catalysis.

Main Methods:

X-ray crystallography to 1.95-A resolution.
Flash-freezing of enzyme crystals soaked with pyruvate.
Structure determination of the covalent adduct.

Main Results:

A protonated carbinolamine intermediate was trapped, formed by pyruvate's nucleophilic attack on Lys-133.
This intermediate is stabilized by hydrogen bonds with active site residues, including Glu-45.
Phe-135 interacts with the pyruvate methyl group, ensuring stereospecific addition.
Lys-133 exists as an epsilon-ammonium salt group in the native structure.

Conclusions:

The study reveals a Schiff base precursor intermediate in KDPG aldolase catalysis.
General base catalysis by Glu-45 and stereospecificity mediated by Phe-135 are key features.
Nucleophilic activation involves proton transfer within a zwitterionic Glu-45/Lys-133 pair, requiring side chain rearrangement.