The three states of pyruvate, phosphate dikinase (unphosphorylated, monophosphorylated, and diphosphorylated) as it converts pyruvate to phosphoenolpyruvate (PEP). Pi = phosphate group. E-His = histidine residue of the enzyme.
ATP + pyruvate + phosphate AMP + phosphoenolpyruvate + diphosphate
This enzyme has been studied primarily in plants, but it has been studied in some bacteria as well.[1] It is a key enzyme in gluconeogenesis and photosynthesis that is responsible for reversing the reaction performed by pyruvate kinase in Embden-Meyerhof-Parnas glycolysis. It should not be confused with pyruvate, water dikinase.
The systematic name of this enzyme class is ATP:pyruvate, phosphate phosphotransferase. Other names in common use include pyruvate, orthophosphate dikinase, pyruvate-phosphate dikinase (phosphorylating), pyruvate phosphate dikinase, pyruvate-inorganic phosphate dikinase, pyruvate-phosphate dikinase, pyruvate-phosphate ligase, pyruvic-phosphate dikinase, pyruvic-phosphate ligase, pyruvate, Pi dikinase, and PPDK.
Reaction mechanism
PPDK catalyses the conversion of pyruvate to phosphoenolpyruvate (PEP), consuming 1 molecule of ATP, and producing one molecule of AMP in the process. The mechanism consists of 3 reversible reactions:[2]
The enzyme PPDK binds to ATP, to produce AMP and a diphosphorylated PPDK.
Phosphorylated PPDK binds to pyruvate, producing phosphoenolpyruvate, and regenerating PPDK.
The reaction is similar to the reaction catalysed by pyruvate kinase, which also converts pyruvate to PEP.[3] However, pyruvate kinase catalyses an irreversible reaction, and does not consume ATP. By contrast, PPDK catalyses a reversible reaction, and consumes 1 molecule of ATP for each molecule of pyruvate converted.
Currently, the details of each mechanistic step is unknown[3]
There are two different reaction centres about 45 Angstroms apart, in which different substrates bind.[5] The nucleotide (ATP) binding site is on the N-terminus, has 240 amino acids, and a characteristic ATP-grasp. The pyruvate/PEP binding site is on the C-terminus, has 340 amino acids, and an α/β-barrel fold. There is also a central domain, which contains His455, the primary residue responsible for catalysis. His455 is the phosphoryl acceptor or donor residue.[3] The structure of the enzyme suggests that the His455 arm undergoes a swivelling motion to shuttle a phosphoryl group between the two reaction centres.[6] During this swivelling, the central domain rotates at least 92 degrees, and translates 0.5 Angstroms.[7]
Studies of crystal structures of PPDK show that the central domain is located in different proximity to the two other domains depending on the source of the enzyme.[7] In maize, it is closer to the C-terminal, while in Clostridium symbiosum, it is closer to the N-terminal.
Research has shown that the PPDK binding mechanisms are similar to that of D-Ala-D-Ala ligase and pyruvate kinase.[5] In particular, PPDK is very similar to pyruvate kinase, which also catalyses the conversion of pyruvate to phosphoenolpyruvate; however, it does so without a phosphorylated-enzyme intermediate.[3] Though their amino acid sequences are different, residues key to catalysis are preserved in both enzymes. Point-mutagenesis experiments have shown that catalytic residues include Arg561, Arg617, Glu745, Asn768, and Cys831 (numbering relative to the C, symbiosum protein, PDB: 1KBL, 1KC7).[3]
PPDK is used in the C4 pathway, to improve the efficiency of carbon dioxide fixation.[8] In environments where there is a lot of light, the rate of photosynthesis in plants is limited by the rate of carbon dioxide (CO2) uptake. This can be improved by using a series of chemical reactions to transport CO2 from mesophyll cells (which are located on the outside of a leaf) to bundle sheath cells (which are located inside the cells). PPDK converts pyruvate to PEP, which reacts with CO2 to produce oxaloacetate. When CO2 is released in the bundle sheath cells, pyruvate is regenerated, and the cycle continues.[8]
Though the reaction catalysed by PPDK is reversible, PEP is favoured as the product in biological conditions. This is due to the basicpH in the stroma, where the reaction occurs, as well as high concentrations of adenylate kinase and pyrophosphatase. Because these two enzymes catalyse exergonic reactions involving AMP, and disphosphate, respectively, they drive the PPDK-catalysed reaction forward.[9] Because PPDK consumes ATP, the C4 pathway is unfavourable for plants in environments with little access to light, as they are unable to produce large quantities of ATP.[8]
PPDK is highly abundant in C4 leaves, comprising up to 10% of total protein.[10] Research has shown that the enzyme is about 96% identical in different species of plants. Hybridization experiments revealed that the genetic differences correlate with the extent to which the plants perform the C4 pathway – the uncommon sequences exist in plants which also display C3 characteristics.[11] PPDK is also found in small quantities in C3 plants. Evolutionary history suggests that it once had a role in glycolysis like the similar pyruvate kinase, and eventually evolved into the C4 pathway.[10]
Besides plants, PPDK is also found in the parasitic ameoba Entamoeba histolytica (P37213) and the bacteria Clostridium symbiosum (P22983; as well as other bacteria).[12] In those two organisms PPDK functions similarly to (and sometimes in place of) pyruvate kinase, catalyzing the reaction in the ATP-producing direction as a part of glycolysis. Inhibitors for the Entamoeba PPDK have been proposed as amebicides against this organism.[13]
Regulation
PPDK is inactivated when PPDK Regulatory Protein (PDRP) phosphorylates Thr456. PDRP both activates and inactivates PPDK.
Plant PPDK is regulated by the pyruvate, phosphate dikinase regulatory protein (PDRP).[4] When levels of light are high, PDRP dephosphorylates Thr456 on PPDK using AMP, thus activating the enzyme.[10] PDRP deactivates PPDK by phosphorylating the same threonineresidue, using diphosphate. PDRP is a unique regulator because it catalyses both activation and deactivation of PPDK, through two different mechanisms.[10]
Research on maize PPDK suggests that introns, terminator sequences, and perhaps other enhancer sequences, act cooperatively to increase the level of functional and stable mRNA. PPDK cDNA was expressed only slightly in transgenic rice, compared to intact DNA which saw significant expression.[14]
Glycolysis is the metabolic pathway that converts glucose into pyruvate and, in most organisms, occurs in the liquid part of cells. The free energy released in this process is used to form the high-energy molecules adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide (NADH). Glycolysis is a sequence of ten reactions catalyzed by enzymes.
In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. As a result, kinase produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.
Gluconeogenesis (GNG) is a metabolic pathway that results in the biosynthesis of glucose from certain non-carbohydrate carbon substrates. It is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms. In vertebrates, gluconeogenesis occurs mainly in the liver and, to a lesser extent, in the cortex of the kidneys. It is one of two primary mechanisms – the other being degradation of glycogen (glycogenolysis) – used by humans and many other animals to maintain blood sugar levels, avoiding low levels (hypoglycemia). In ruminants, because dietary carbohydrates tend to be metabolized by rumen organisms, gluconeogenesis occurs regardless of fasting, low-carbohydrate diets, exercise, etc. In many other animals, the process occurs during periods of fasting, starvation, low-carbohydrate diets, or intense exercise.
Crassulacean acid metabolism, also known as CAM photosynthesis, is a carbon fixation pathway that evolved in some plants as an adaptation to arid conditions that allows a plant to photosynthesize during the day, but only exchange gases at night. In a plant using full CAM, the stomata in the leaves remain shut during the day to reduce evapotranspiration, but they open at night to collect carbon dioxide and allow it to diffuse into the mesophyll cells. The CO2 is stored as four-carbon malic acid in vacuoles at night, and then in the daytime, the malate is transported to chloroplasts where it is converted back to CO2, which is then used during photosynthesis. The pre-collected CO2 is concentrated around the enzyme RuBisCO, increasing photosynthetic efficiency. This mechanism of acid metabolism was first discovered in plants of the family Crassulaceae.
C4 carbon fixation or the Hatch–Slack pathway is one of three known photosynthetic processes of carbon fixation in plants. It owes the names to the 1960s discovery by Marshall Davidson Hatch and Charles Roger Slack.
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. Pyruvate kinase was inappropriately named before it was recognized that it did not directly catalyze phosphorylation of pyruvate, which does not occur under physiological conditions. Pyruvate kinase is present in four distinct, tissue-specific isozymes in animals, each consisting of particular kinetic properties necessary to accommodate the variations in metabolic requirements of diverse tissues.
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 that occur in animals. It takes part in gluconeogenesis, the urea cycle, the glyoxylate cycle, amino acid synthesis, fatty acid synthesis and the citric acid cycle.
Phosphoenolpyruvate is the carboxylic acid derived from the enol of pyruvate and phosphate. It exists as an anion. PEP is an important intermediate in biochemistry. It has the highest-energy phosphate bond found in organisms, and is involved in glycolysis and gluconeogenesis. In plants, it is also involved in the biosynthesis of various aromatic compounds, and in carbon fixation; in bacteria, it is also used as the source of energy for the phosphotransferase system.
In biochemistry, mixed acid fermentation is the metabolic process by which a six-carbon sugar is converted into a complex and variable mixture of acids. It is an anaerobic (non-oxygen-requiring) fermentation reaction that is common in bacteria. It is characteristic for members of the Enterobacteriaceae, a large family of Gram-negative bacteria that includes E. coli.
Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:
Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) (EC 1.1.1.40) or NADP-malic enzyme (NADP-ME) is an enzyme that catalyzes the chemical reaction in the presence of a bivalent metal ion:
In enzymology, a phosphoglucan, water dikinase (EC 2.7.9.5) is an enzyme that catalyzes the chemical reaction
Phosphoribulokinase (PRK) (EC 2.7.1.19) is an essential photosynthetic enzyme that catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate (RuP) into ribulose 1,5-bisphosphate (RuBP), both intermediates in the Calvin Cycle. Its main function is to regenerate RuBP, which is the initial substrate and CO2-acceptor molecule of the Calvin Cycle. PRK belongs to the family of transferase enzymes, specifically those transferring phosphorus-containing groups (phosphotransferases) to an alcohol group acceptor. Along with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase is unique to the Calvin Cycle. Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. Much initial work on PRK was done with spinach leaf extracts in the 1950s; subsequent studies of PRK in other photosynthetic prokaryotic and eukaryotic organisms have followed. The possibility that PRK might exist was first recognized by Weissbach et al. in 1954; for example, the group noted that carbon dioxide fixation in crude spinach extracts was enhanced by the addition of ATP. The first purification of PRK was conducted by Hurwitz and colleagues in 1956.
ATP + Mg2+ - D-ribulose 5-phosphate ADP + D-ribulose 1,5-bisphosphate
In enzymology, a pyruvate, water dikinase (EC 2.7.9.2) is an enzyme that catalyzes the chemical reaction
Dikinases are a category of enzymes that catalyze the chemical reaction
3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.
(Pyruvate, phosphate dikinase)-phosphate phosphotransferase is an enzyme with systematic name (pyruvate, phosphate dikinase) phosphate:phosphate phosphotransferase. This enzyme catalyses the following chemical reaction
(Pyruvate, phosphate dikinase) kinase is an enzyme with systematic name ADP:(pyruvate, phosphate dikinase) phosphotransferase. This enzyme catalyses the following chemical reaction
(Pyruvate, water dikinase) kinase is an enzyme with systematic name ADP:(pyruvate, water dikinase) phosphotransferase. This enzyme catalyses the following chemical reaction
References
↑ Pocalyko DJ, Carroll LJ, Martin BM, Babbitt PC, Dunaway-Mariano D (December 1990). "Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs". Biochemistry. 29 (48): 10757–65. doi:10.1021/bi00500a006. PMID2176881.
1 2 3 4 5 Herzberg O, Chen CC, Liu S, Tempczyk A, Howard A, Wei M, etal. (January 2002). "Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis". Biochemistry. 41 (3): 780–7. doi:10.1021/bi011799+. PMID11790099.
1 2 Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H (February 2005). "Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion". Biochemistry. 44 (4): 1136–44. doi:10.1021/bi0484522. PMID15667207.
1 2 3 Berg J, Tymoczko J, Stryer L (2012). "The Calvin Cycle and the Pentose Phosphate Pathway". Biochemistry (7thed.). New York: W.H Freeman. pp.599–600. ISBN9780716787242.
↑ Chastain C (2010). "Structure, Function, and Post-Translational Regulation of C4 Pyruvate Orthophosphate Dikinase". In Raghavendra A (ed.). C4 Photosynthesis and Related CO2 Concentrating Mechanisms. Springer. pp.301–305. ISBN9789048194063.
↑ Rosche E, Streubel M, Westhoff P (October 1994). "Primary structure of the photosynthetic pyruvate orthophosphate dikinase of the C3 plant Flaveria pringlei and expression analysis of pyruvate orthophosphate dikinase sequences in C3, C3-C4 and C4 Flaveria species". Plant Molecular Biology. 26 (2): 763–9. doi:10.1007/bf00013761. PMID7948930. S2CID23276817.
↑ Stephen P, Vijayan R, Bhat A, Subbarao N, Bamezai RN (September 2008). "Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors". Journal of Computer-Aided Molecular Design. 22 (9): 647–60. Bibcode:2008JCAMD..22..647S. doi:10.1007/s10822-007-9130-2. PMID17710553. S2CID25026913.
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