phosphoribulokinase | |||||||||
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Identifiers | |||||||||
EC no. | 2.7.1.19 | ||||||||
CAS no. | 9030-60-8 | ||||||||
Databases | |||||||||
IntEnz | IntEnz view | ||||||||
BRENDA | BRENDA entry | ||||||||
ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
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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. [1] 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. [2] Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. [3] 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. [3] [4] The first purification of PRK was conducted by Hurwitz and colleagues in 1956. [5] [6] [7]
ATP + Mg2+ - D-ribulose 5-phosphate ADP + D-ribulose 1,5-bisphosphate
The two substrates of PRK are ATP and D-ribulose 5-phosphate, whereas its two products are ADP and D-ribulose 1,5-bisphosphate. PRK activity requires the presence of a divalent metal cation like Mg2+, as indicated in the reaction above. [3]
The structure of PRK is different in prokaryotes and eukaryotes. Prokaryotic PRK's typically exist as octamers of 32 kDa subunits, while eukaryotic PRK's are often dimers of 40 kDa subunits. [8] [9] Structural determinations for eukaryotic PRK have yet to be conducted, but prokaryotic PRK structures are still useful for rationalizing the regulation and mechanism of PRK. As of 2018, only two crystal structures have been resolved for this class of enzymes in Rhodobacter sphaeroides and Methanospirillum hungatei , with the respective PDB accession codes 1A7J and 5B3F.
In Rhodobacter sphaeroides, PRK (or RsPRK) exists as a homooctomer with protomers composed of seven-stranded mixed β-sheets, seven α-helices, and an auxiliary pair of anti-parallel β-strands. [10] The RsPRK subunit exhibits a protein folding analogous to the folding of nucleotide monophosphate (NMP) kinases. [3] Mutagenesis studies suggest that either Asp 42 or Asp 169 acts as the catalytic base that deprotonates the O1 hydroxyl oxygen on RuP for nucleophilic attack of ATP, while the other acts a ligand for a metal cation like Mg2+ (read mechanism below for more details). [10] Other residues present at the active site for RsPRK include His 45, Arg 49, Arg 168, and Arg 173, which are purportedly involved in RuP binding. [10] (See image at right).
In archaeal PRK of Methanospirillum hungatei, PRK (or MhPRK) exists as a homodimer of two protomers, each consisting of eight-stranded mixed β-sheets surrounded by α-helices and β-strands—similar to the structure of bacterial PRK from R. sphaeroides (see info. box above). [11] Although their quaternary structures differ and they have low amino acid sequence identity, MhPRK and RsPRK have structurally similar N-terminal domains as well as sequentially conserved residues like His 55, Lys 151, and Arg 154. [11]
PRK catalyzes the phosphorylation of RuP into RuBP. A catalytic residue in the enzyme (i.e. aspartate in RsPRK) deprotonates the O1 hydroxyl oxygen on RuP and activates it for nucleophilic attack of the γ-phosphoryl group of ATP. [10] As the γ-phosphoryl group is transferred from ATP to RuP, its stereochemistry inverts. [12] To allow for such inversion, the catalytic mechanism of PRK must not involve a phosphoryl-enzyme intermediate. [12]
Some studies suggest that both substrates (ATP and RuP) bind simultaneously to PRK and form a ternary complex. Others suggest that the substrate addition is sequential; the particular order by which substrates are added is still disputed, and may in fact, vary for different organisms. [13] [14] In addition to binding its substrates, PRK also requires ligation to divalent metal cations like Mg2+ or Mn2+ for activity; Hg2+ has been demonstrated to inactivate the enzyme. [3] [15]
PRK shows high specificity for ribulose 5-phosphate. It does not act on any of the following substrates: D-xylulose 5-phosphate, fructose 6-phosphate, and sedoheptulose 7-phosphate. [15] However, at high concentrations, PRK may sometimes phosphorylate ribose 5-phosphate, a compound upstream the RuBP regeneration step in the Calvin Cycle. [15] Furthermore, PRK isolated from Alcaligenes eutrophus has been shown to use uridine triphosphate (UTP) and guanosine triphosphate (GTP) as alternative substrates to ATP. [8] [3]
The phosphorylation reaction proceeds with maximal velocity at pH 7.9, with no detectable activity at pH's below 5.5 or above 9.0. [15]
The mechanisms by which prokaryotic and eukaryotic PRK's are regulated vary. Prokaryotic PRK's are typically subject to allosteric regulation while eukaryotic PRK's are often regulated by reversible thiol/disulfide exchange. [16] These differences are likely due to structural differences in their C-terminal domains [11]
NADH is known to stimulate PRK activity, while AMP and phosphoenolpyruvate (PEP) are known to inhibit activity. [3] AMP has been shown to be involved in competitive inhibition in Thiobacillus ferrooxidans PRK. [17] On the other hand, PEP acts as a non-competitive inhibitor of PRK. [18]
Eukaryotic PRK is typically regulated through the reversible oxidation/reduction of its cysteine sulfhydryl groups, but studies suggests that its activity can be regulated by other proteins or metabolites in the chloroplast. Of such metabolites, 6-phosphogluconate has been shown to be the most effective inhibitor of eukaryotic PRK by competing with RuP for the enzyme's active site. [19] This phenomenon may arise from the similarity in molecular structure between 6-phosphogluconate and RuP.
More recent work on the regulation of eukaryotic PRK has focused on its ability to form multi-enzyme complexes with other Calvin cycle enzymes such as glyceraldehyde 3-phosphate dehydrogenase (G3PDH) or RuBisCo. [20] In Chlamydomonas reinhardtii , chloroplast PRK and G3PDH exist as a bi-enzyme complex of 2 molecules of dimeric PRK and 2 molecules of tetrameric G3PDH thorough association by an Arg 64 residue, which may potentially transfer information between the two enzymes as well. [21]
Multi-enzyme complexes are likely to have more intricate regulatory mechanisms, and studies have already probed such processes. For example, it has been shown that PRK-glyceraldehyde 3-phosphate dehydrogenase complexes in Scenedesmus obliquus only dissociate to release activated forms of its constituent enzymes in the presence of NADPH, dithiothreitol (DTT), and thioredoxin. [22] Another topic of interest has been to compare the relative levels of PRK activity for when it is complexed to when it is not. For different photosynthetic eukaryotes, the enzyme activity of complexed PRK may be enhanced as opposed to free PRK, and vice versa. [23] [24]
The systematic name of this enzyme class is ATP:D-ribulose-5-phosphate 1-phosphotransferase. Other names in common use include phosphopentokinase, ribulose-5-phosphate kinase, phosphopentokinase, phosphoribulokinase (phosphorylating), 5-phosphoribulose kinase, ribulose phosphate kinase, PKK, PRuK, and PRK.
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.
In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology. Protein phosphorylation often activates many enzymes.
Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Ribulose 1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis, notably as the principal CO2 acceptor in plants. It is a colourless anion, a double phosphate ester of the ketopentose called ribulose. Salts of RuBP can be isolated, but its crucial biological function happens in solution. RuBP occurs not only in plants but in all domains of life, including Archaea, Bacteria, and Eukarya.
In organic chemistry, a tetrose is a monosaccharide with 4 carbon atoms. They have either an aldehyde functional group in position 1 (aldotetroses) or a ketone group in position 2 (ketotetroses).
The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into glucose. The Calvin cycle is present in all photosynthetic eukaryotes and also many photosynthetic bacteria. In plants, these reactions occur in the stroma, the fluid-filled region of a chloroplast outside the thylakoid membranes. These reactions take the products of light-dependent reactions and perform further chemical processes on them. The Calvin cycle uses the chemical energy of ATP and reducing power of NADPH from the light dependent reactions to produce sugars for the plant to use. These substrates are used in a series of reduction-oxidation (redox) reactions to produce sugars in a step-wise process; there is no direct reaction that converts several molecules of CO2 to a sugar. There are three phases to the light-independent reactions, collectively called the Calvin cycle: carboxylation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.
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. With the chemical formula H(O)CCH(OH)CH2OPO32-, this anion is a monophosphate ester of glyceraldehyde.
Aldolase A, also known as fructose-bisphosphate aldolase, is an enzyme that in humans is encoded by the ALDOA gene on chromosome 16.
Methylotrophs are a diverse group of microorganisms that can use reduced one-carbon compounds, such as methanol or methane, as the carbon source for their growth; and multi-carbon compounds that contain no carbon-carbon bonds, such as dimethyl ether and dimethylamine. This group of microorganisms also includes those capable of assimilating reduced one-carbon compounds by way of carbon dioxide using the ribulose bisphosphate pathway. These organisms should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide. Some methylotrophs can degrade the greenhouse gas methane, and in this case they are called methanotrophs. The abundance, purity, and low price of methanol compared to commonly used sugars make methylotrophs competent organisms for production of amino acids, vitamins, recombinant proteins, single-cell proteins, co-enzymes and cytochromes.
3-Phosphoglyceric acid (3PG, 3-PGA, or PGA) is the conjugate acid of 3-phosphoglycerate or glycerate 3-phosphate (GP or G3P). This glycerate is a biochemically significant metabolic intermediate in both glycolysis and the Calvin-Benson cycle. The anion is often termed as PGA when referring to the Calvin-Benson cycle. In the Calvin-Benson cycle, 3-phosphoglycerate is typically the product of the spontaneous scission of an unstable 6-carbon intermediate formed upon CO2 fixation. Thus, two equivalents of 3-phosphoglycerate are produced for each molecule of CO2 that is fixed. In glycolysis, 3-phosphoglycerate is an intermediate following the dephosphorylation (reduction) of 1,3-bisphosphoglycerate.
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:
Phosphoglycerate kinase is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP :
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Fructose 2,6-bisphosphate, abbreviated Fru-2,6-P2, is a metabolite that allosterically affects the activity of the enzymes phosphofructokinase 1 (PFK-1) and fructose 1,6-bisphosphatase (FBPase-1) to regulate glycolysis and gluconeogenesis. Fru-2,6-P2 itself is synthesized and broken down in either direction by the integrated bifunctional enzyme phosphofructokinase 2 (PFK-2/FBPase-2), which also contains a phosphatase domain and is also known as fructose-2,6-bisphosphatase. Whether the kinase and phosphatase domains of PFK-2/FBPase-2 are active or inactive depends on the phosphorylation state of the enzyme.
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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-phosphate (G3P). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism.
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