1. Nomenclature

2. Enzyme structure

3. Enzyme mechanism

4. Evolutionary significance
    History 

5. References

6. Further reading

7. External links

In enzymology, a 2-dehydro-3-deoxy-phosphogluconate aldolase ({{EC number|4.1.2.14}}), commonly known as KDPG aldolase, is an enzyme that catalyzes the chemical reaction

2-dehydro-3-deoxy-D-gluconate 6-phosphate pyruvate + D-glyceraldehyde 3-phosphate

Hence, this enzyme primarily has one substrate, 2-dehydro-3-deoxy-D-gluconate 6-phosphate, and two products, pyruvate and D-glyceraldehyde 3-phosphate.

This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. It is used in the Entner–Doudoroff pathway in prokaryotes, feeding into glycolysis. 2-dehydro-3-deoxy-phosphogluconate aldolase is one of the two enzymes distinguishing this pathway from the more commonly known Embden–Meyerhof–Parnas pathway.^[1] This enzyme also participates in following 3 metabolic pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and arginine and proline metabolism.

In addition to the cleavage of 2-dehydro-3-deoxy-D-gluconate 6-phosphate, it is also found to naturally catalyze Schiff base formation between a lysine E-amino acid group and carbonyl compounds, decarboxylation of oxaloacetate, and exchange of solvent protons with the methyl hydrogen atoms of pyruvate.^[2]

Nomenclature

The systematic name of this enzyme class is 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming). Other names in common use include:

• KDPG aldolase
• phospho-2-keto-3-deoxygluconate aldolase
• phospho-2-keto-3-deoxygluconic aldolase
• 2-keto-3-deoxy-6-phosphogluconic aldolase
• 2-keto-3-deoxy-6-phosphogluconate aldolase
• 6-phospho-2-keto-3-deoxygluconate aldolase
• ODPG aldolase, 2-oxo-3-deoxy-6-phosphogluconate aldolase
• 2-keto-3-deoxygluconate-6-P-aldolase
• 2-keto-3-deoxygluconate-6-phosphate aldolase
• 2-dehydro-3-deoxy-D-gluconate-6-phosphate
• D-glyceraldehyde-3-phosphate-lyase

Enzyme structure

KDPG Aldolase was recently determined to be a trimer through crystallographic three-fold symmetry, with 225 residues.^[2][3] The enzyme was determined to have a molecular weight of 23,942.^[4] The trimer is stabilized primarily through hydrophobic interactions. The molecule has tertiary folding similar to triosephosphate isomerase and the A-domain of pyruvate kinase, forming an eight strand α/β-barrel structure.^[3][5] The α/β-barrel structure is capped on one side by the N-terminal helix. The other side, the carboxylic side, contains the active site.^[6] Each subunit contains a phosphate-ion bound in position of the aldolase biding site.^[9] It has been found that there are four cysteinyl groups present in each subunit, with two readily accessible and two buried in the subunit.^[7]

The active site contains the zwitterionic pair Glu-45/Lys-133.^[11] The Lysine, which is involved in the formation of the Schiff base is coordinated by a phosphate ion and two solvent water molecules.^[6][9] The first water molecule serves as a shuttle between the Glutamate and the substrate, staying bound to the enzyme throughout the catalytic cycle.^[9] The second water molecule is a product of the dehydration of the carbinolamine that leads to the formation of the Schiff base.^[9] It also functions as the nucleophile during hydrolysis of the enzyme-product Schiff base, leading to the release of pyruvate.^[9]

As of late 2007, 13 structures have been solved for this class of enzymes, with PDB accession codes {{PDB link|1EUA}}, {{PDB link|1EUN}}, {{PDB link|1FQ0}}, {{PDB link|1FWR}}, {{PDB link|1KGA}}, {{PDB link|1MXS}}, {{PDB link|1WA3}}, {{PDB link|1WAU}}, {{PDB link|1WBH}}, {{PDB link|2C0A}}, {{PDB link|2NUW}}, {{PDB link|2NUX}}, and {{PDB link|2NUY}}.

Enzyme mechanism

One of the reactions KDPG Aldolase catalyzes, as in the Entner–Doudoroff pathway, is the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) into pyruvate and D-glyceraldehyde-3-phosphate.^[8][9] This occurs through a stereospecific retro-aldol cleavage.^[10] A proton transfer between the zwitterionic pair Glu-45/Lys-133 in the active site activates Lysine to serve as the nucleophile in the first step and Glutamate to aid in the base catalysis involved in the carbon-carbon cleavage.^[8] Lysine Residue 133 serves as the nucleophile and attacks the carbonyl group of 2-Keto-3-deoxy-6-phosphogluconate to form a protonated carbinolamine intermediate, also known as a Schiff base intermediate.^[10][8][9] The intermediate is stabilized by hydrogen bonding with residues in the active site.^[8] A three carbon residue, glyceraldehyde 3-phosphate, is cleaved off through base catalysis with a water molecule and residue Glu-45.^[10][8] The pyruvate is generated through the nucleophilic attack of water on the Schiff-base to reform a ketone. Aromatic interaction with Phe-135 ensures the stereospecific addition involved in the reverse process.^[8]

KDPG aldolase has also been shown to catalyze the exchange of hydrogen atoms of the methyl groups of pyruvate with protons of the solvent.^[9]

Evolutionary significance

History

Arguments have been made for both the convergent and divergent evolution of α/β-barrel structured enzymes such as KDPG Aldolase, triosephosphate isomerase, and the A-domain of pyruvate kinase.

Convergent evolution can lead to geometrically similar active sites while each enzyme has a distinct backbone conformation. Convergence to a common backbone structure, as is the case here however, has not been observed, although it is argues that it might be possible for a symmetrically repetitive structure as the one observed here.^[11] The similarity in the folding of the three enzymes and the exceptional symmetry commonly suggests divergent evolution from a common ancestor. The functional similarity of the enzymes remains the strongest argument for divergent evolution.^[11] All three enzymes activate a C–H bond adjacent to a carbonyl group. The active sites are located at the carboxylic ends of the β strands. Such congruence is in favor of divergent evolution.

Should the divergent evolution hypothesis prevail, this would suggest the existence of a class of enzymes with unrelated amino acid sequences yet analogous symmetrical structure and folding.^[11]

KDPG aldolase has limited utility due to its high specificity for its natural substrates in the cleavage of KDPG and the reverse addition of D-glyceraldehyde-3-phosphate and pyruvate.^[12] In vitro evolution has allowed KDPG aldolase to be converted into a more efficient aldolase with altered substrate specificity and stereoselectivity thereby improving its utility in asymmetric synthesis.^[13] Rather than modifying the recognition site, the substrate is modified by moving the active site lysine from one β strand to a neighboring one.^[13][14] The evolved aldolase is capable of accepting both D- and L-glyceraldehyde in their non-phosphorylated form.^[15]

References

Further reading

• {{cite journal |vauthors=Meloche HP, Wood WA | year = 1964 | title = Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase | journal = J. Biol. Chem. | volume = 239 | pages = 3515–3518 | pmid=14245411}}

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