Glyoxylate and dicarboxylate metabolism
Encyclopedia
Glyoxylate and dicarboxylate metabolism describes a variety of reactions involving glyoxylate or dicarboxylates. Glyoxylate is the conjugate base of glyoxylic acid
, and within a buffered environment of known pH
such as the cell cytoplasm
these terms can be used almost interchangeably, as the gain or loss of a hydrogen ion
is all that distinguishes them can occur in the aqueous environment at any time. Likewise dicarboxylates are the conjugate bases of dicarboxylic acid
s, a general class of organic compounds containing two carboxylic acid
groups, such as oxalic acid
or succinic acid
.
A compact graphical description of major biochemical reactions involved can be found at KEGG This provides information on the relevant enzyme
s and details the relationship with several other metabolic processes: glycine, serine, and threonine metabolism which provides hydroxypyruvate and glyoxylate, purine metabolism
which provides glyoxylate, pyruvate metabolism which provides (S)-malate
and formate
, carbon fixation
which consumes 3-phospho-D-glycerate and provides D-ribulose
1,5-P2, ascorbate and aldarate metabolism which shares tartronate-semialdehyde, nitrogen metabolism which shares formate
, pyruvate metabolism and the citrate cycle which share oxaloacetate, and vitamin B6 metabolism
which consumes glycolaldehyde
.
The glyoxylate cycle
describes an important subset of these reactions involved in biosynthesis of carbohydrates from fatty acids or two-carbon precursors which enter the system as acetyl-coenzyme A. Its crucial enzymes are isocitrate lyase
and malate synthase
. However, alternate pathways have been proposed in organisms lacking isocitrate lyase.
Glyoxylic acid
Glyoxylic acid or oxoacetic acid is an organic compound. Together with acetic acid, glycolic acid, and oxalic acid, glyoxylic acid is one of the C2 carboxylic acids. It is a colourless solid that occurs naturally and is useful industrially....
, and within a buffered environment of known pH
PH
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...
such as the cell cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...
these terms can be used almost interchangeably, as the gain or loss of a hydrogen ion
Hydrogen ion
Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes.Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions....
is all that distinguishes them can occur in the aqueous environment at any time. Likewise dicarboxylates are the conjugate bases of dicarboxylic acid
Dicarboxylic acid
Dicarboxylic acids are organic compounds that contain two carboxylic acid functional groups. In molecular formulae for dicarboxylic acids, these groups are often written as HOOC-R-COOH, where R may be an alkyl, alkenyl, alkynyl, or aryl group...
s, a general class of organic compounds containing two carboxylic acid
Carboxylic acid
Carboxylic acids are organic acids characterized by the presence of at least one carboxyl group. The general formula of a carboxylic acid is R-COOH, where R is some monovalent functional group...
groups, such as oxalic acid
Oxalic acid
Oxalic acid is an organic compound with the formula H2C2O4. This colourless solid is a dicarboxylic acid. In terms of acid strength, it is about 3,000 times stronger than acetic acid. Oxalic acid is a reducing agent and its conjugate base, known as oxalate , is a chelating agent for metal cations...
or succinic acid
Succinic acid
Succinic acid is a dicarboxylic acid. Succinate plays a biochemical role in the citric acid cycle. The name derives from Latin succinum, meaning amber, from which the acid may be obtained....
.
A compact graphical description of major biochemical reactions involved can be found at KEGG This provides information on the relevant enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s and details the relationship with several other metabolic processes: glycine, serine, and threonine metabolism which provides hydroxypyruvate and glyoxylate, purine metabolism
Purine metabolism
-Biosynthesis:Purines are biologically synthesized as nucleotides and in particular as ribotides, i.e. bases attached to ribose 5-phosphate. A key regulatory step is the production of 5-phospho-α-D-ribosyl 1-pyrophosphate by PRPP synthetase, which is activated by inorganic phosphate and...
which provides glyoxylate, pyruvate metabolism which provides (S)-malate
Malate
Malate is the ionized form of malic acid. It is an important chemical compound in biochemistry. In the C4 carbon fixation process, malate is a source of CO2 in the Calvin cycle....
and formate
Formate
Formate or methanoate is the ion CHOO− or HCOO− . It is the simplest carboxylate anion. It is produced in large amounts in the hepatic mitochondria of embryonic cells and in cancer cells by the folate cycle Formate or methanoate is the ion CHOO− or HCOO− (formic acid minus one hydrogen ion). It...
, carbon fixation
Carbon fixation
In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that...
which consumes 3-phospho-D-glycerate and provides D-ribulose
Ribulose
Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. It has chemical formula 5105. Two enantiomers are possible, D-ribulose and L-ribulose . D-Ribulose is the diastereomer of D-xylulose.Ribulose sugars are composed in the...
1,5-P2, ascorbate and aldarate metabolism which shares tartronate-semialdehyde, nitrogen metabolism which shares formate
Formate
Formate or methanoate is the ion CHOO− or HCOO− . It is the simplest carboxylate anion. It is produced in large amounts in the hepatic mitochondria of embryonic cells and in cancer cells by the folate cycle Formate or methanoate is the ion CHOO− or HCOO− (formic acid minus one hydrogen ion). It...
, pyruvate metabolism and the citrate cycle which share oxaloacetate, and vitamin B6 metabolism
Vitamin B6
Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group. Several forms of the vitamin are known, but pyridoxal phosphate is the active form and is a cofactor in many reactions of amino acid metabolism, including transamination, deamination, and decarboxylation...
which consumes glycolaldehyde
Glycolaldehyde
Glycolaldehyde is the smallest possible molecule that contains both an aldehyde group and a hydroxyl group. It is the only possible diose, a 2-carbon monosaccharide, although a diose is not strictly a saccharide...
.
The glyoxylate cycle
Glyoxylate cycle
The glyoxylate cycle, a variation of the Tricarboxylic Acid Cycle, is an anabolic metabolic pathway occurring in plants, bacteria, protists, fungi and several microorganisms, such as E. coli and yeast. The glyoxylate cycle centers on the conversion of acetyl-CoA to succinate for the synthesis of...
describes an important subset of these reactions involved in biosynthesis of carbohydrates from fatty acids or two-carbon precursors which enter the system as acetyl-coenzyme A. Its crucial enzymes are isocitrate lyase
Isocitrate lyase
Isocitrate lyase , or ICL, is an enzyme in the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate. Together with malate synthase, it bypasses the two decarboxylation steps of the tricarboxylic acid cycle and is used by bacteria, fungi, and plants.The systematic...
and malate synthase
Malate synthase
In enzymology, a malate synthase is an enzyme that catalyzes the chemical reactionThe 3 substrates of this enzyme are acetyl-CoA, H2O, and glyoxylate, whereas its two products are -malate and CoA....
. However, alternate pathways have been proposed in organisms lacking isocitrate lyase.