enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

catalyzes Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quick ...

chemical reaction A chemical reaction is a process that leads to the chemistry, chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an Gibbs free energy, ...

lyase In biochemistry, a lyase is an enzyme that catalyzes the breaking (an elimination reaction) of various chemical bonds by means other than hydrolysis (a substitution reaction) and oxidation Redox ( , , reduction–oxidation or oxidatio ...

aldehyde In organic chemistry, an aldehyde () (lat. ''al''cohol ''dehyd''rogenatum, dehydrogenated alcohol) is an organic compound containing a functional group with the structure . The functional group itself (without the "R" side chain) can be referred ...

Entner–Doudoroff pathway The Entner–Doudoroff pathway (ED Pathway) is a metabolic pathway that is most notable in Gram-negative bacteria, certain Gram-positive bacteria and archaea. Glucose is the substrate in the ED pathway and, through a series of enzyme assisted chemi ...

metabolic pathways In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical ...

pentose phosphate pathway The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt or HMP shunt) is a metabolic pathway parallel to glycolysis. It generates NADPH and pentoses (five-carbon sugars) as well as ribose 5-ph ...

pentose and glucuronate interconversions In chemistry, a pentose is a monosaccharide (simple sugar) with five carbon atoms. The chemical formula of many pentoses is , and their molecular weight is 150.13 g/mol.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 In organic chemistry, a Schiff base (named after Hugo Schiff) is a compound with the general structure ( = alkyl or aryl, but not hydrogen). They can be considered a sub-class of imines, being either secondary ketimines or secondary aldim ...

formation between a

lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. Lysine contains an α-amino group (which is in the protonated form when the lysine is dissolved in water at physiological pH), an α-carboxylic acid group ( ...

ε-amino acid group and carbonyl compounds, decarboxylation of

oxaloacetate Oxaloacetic acid (also known as oxalacetic acid or OAA) is a crystalline organic compound with the chemical formula HO2CC(O)CH2CO2H. Oxaloacetic acid, in the form of its conjugate base oxaloacetate, is a metabolic intermediate in many processes ...

, and exchange of solvent protons with the methyl hydrogen atoms of

pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic ...

.

Nomenclature

The

systematic name A systematic name is a name given in a systematic way to one unique group, organism, object or chemical substance, out of a specific population or collection. Systematic names are usually part of a nomenclature. A semisystematic name or semitrivi ...

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. The enzyme was determined to have a molecular weight of 23,942. The trimer is stabilized primarily through hydrophobic interactions. The molecule has tertiary folding similar to triosephosphate isomerase and the A-domain of

pyruvate kinase Pyruvate kinase is the enzyme involved in the last step of glycolysis. It catalyzes the transfer of a phosphate group from phosphoenolpyruvate (PEP) to adenosine diphosphate (ADP), yielding one molecule of pyruvate and one molecule of ATP. Pyruv ...

, forming an eight strand α/β-barrel structure. 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. Each subunit contains a

phosphate Phosphates are the naturally occurring form of the element phosphorus. In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthop ...

-ion bound in position of the aldolase binding site. It has been found that there are four cysteinyl groups present in each subunit, with two readily accessible and two buried in the subunit. The active site contains the zwitterionic pair Glu-45/ Lys-133. The Lysine, which is involved in the formation of the

Schiff base In organic chemistry, a Schiff base (named after Hugo Schiff) is a compound with the general structure ( = alkyl or aryl, but not hydrogen). They can be considered a sub-class of imines, being either secondary ketimines or secondary aldim ...

is coordinated by a phosphate ion and two solvent water molecules. The first water molecule serves as a shuttle between the Glutamate and the substrate, staying bound to the enzyme throughout the catalytic cycle. The second water molecule is a product of the dehydration of the carbinolamine that leads to the formation of the Schiff base. It also functions as the

nucleophile In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...

during hydrolysis of the enzyme-product Schiff base, leading to the release of pyruvate. As of late 2007, 13

structures A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , and .

Enzyme mechanism

One of the reactions KDPG Aldolase catalyzes, as in the

Entner–Doudoroff pathway The Entner–Doudoroff pathway (ED Pathway) is a metabolic pathway that is most notable in Gram-negative bacteria, certain Gram-positive bacteria and archaea. Glucose is the substrate in the ED pathway and, through a series of enzyme assisted chemi ...

, is the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) into

pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic ...

and D-glyceraldehyde-3-phosphate. This occurs through a stereospecific retro-aldol cleavage. A proton transfer between the zwitterionic pair Glu-45/Lys-133 in the active site activates Lysine to serve as the

nucleophile In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...

in the first step and Glutamate to aid in the base catalysis involved in the carbon-carbon cleavage. 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 In organic chemistry, a Schiff base (named after Hugo Schiff) is a compound with the general structure ( = alkyl or aryl, but not hydrogen). They can be considered a sub-class of imines, being either secondary ketimines or secondary aldim ...

intermediate. The intermediate is stabilized by hydrogen bonding with residues in the active site. A three carbon residue,

glyceraldehyde 3-phosphate Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms.Nelson, D ...

, is cleaved off through base catalysis with a water molecule and residue Glu-45. The

pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic ...

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. KDPG aldolase has also been shown to catalyze the exchange of hydrogen atoms of the methyl groups of

pyruvate Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic ...

with protons of the solvent. Aldolase18916

Evolutionary significance

History

Arguments have been made for both the convergent and

divergent evolution Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, sometimes leading to speciation. Divergent evolution is typically exhibited when two populations become separate ...

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. 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. 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. Directed Evolution 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 Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic ...

. In vitro evolution has allowed KDPG aldolase to be converted into a more efficient

aldolase Fructose-bisphosphate aldolase (), often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphat ...

with altered substrate specificity and stereoselectivity thereby improving its utility in asymmetric synthesis. Rather than modifying the recognition site, the substrate is modified by moving the active site

lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. Lysine contains an α-amino group (which is in the protonated form when the lysine is dissolved in water at physiological pH), an α-carboxylic acid group ( ...

from one β strand to a neighboring one. The evolved aldolase is capable of accepting both D- and L-glyceraldehyde in their non-phosphorylated form.

References

External links

* {{Portal bar, Biology, border=no EC 4.1.2 Enzymes of known structure

Nomenclature

Enzyme structure

Enzyme mechanism

Evolutionary significance

History

References

Further reading

External links