| Plastocyanin | |
|---|---|
 | |
| Identifiers | |
| Symbol | Plastocyanin |
| InterPro | IPR002387 |
| CATH | 3BQV |
| SCOP2 | 3BQV / SCOPe / SUPFAM |
| CDD | cd04219 |
| UniProt Family | |
Plastocyanin is a copper-containing protein that mediates electron-transfer. It is found in a variety of plants, where it participates in photosynthesis. The protein is a prototype of the blue copper proteins, a family of intensely blue-colored metalloproteins. Specifically, it falls into the group of small type I blue copper proteins called "cupredoxins". [1]
In photosynthesis, plastocyanin functions as an electron transfer agent between cytochrome f of the cytochrome b6f complex from photosystem II and P700+ from photosystem I. Cytochrome b6f complex and P700+ are both membrane-bound proteins with exposed residues on the lumen-side of the thylakoid membrane of chloroplasts. Cytochrome f acts as an electron donor while P700+ accepts electrons from reduced plastocyanin. [2]
Plastocyanin was the first of the blue copper proteins to be characterised by X-ray crystallography. [3] [2] [4] It features an eight-stranded antiparallel β-barrel containing one copper center. [3]
Structures of the protein from poplar, algae, parsley, spinach, and French bean plants have been characterized crystallographically. [3] In all cases the binding site is generally conserved. Bound to the copper center are four ligands: the imidazole groups of two histidine residues (His37 and His87), the thiolate of Cys84 and the thioether of Met92. The geometry of the copper binding site is described as a ‘distorted trigonal pyramidal’. The Cu-S (cys) contact is much shorter (207 picometers) than Cu-S (met) (282 pm) bond. The elongated Cu-thioether bond appears to destabilise the CuII state thereby enhancing its oxidizing power. The blue colour (597 nm peak absorption) is assigned to a charge transfer transition from Spπ to Cudx2-y2. [5]
In the reduced form of plastocyanin, His-87 becomes protonated.
While the molecular surface of the protein near the copper binding site varies slightly, all plastocyanins have a hydrophobic surface surrounding the exposed histidine of the copper binding site. In plant plastocyanins, acidic residues are located on either side of the highly conserved tyrosine-83. Algal plastocyanins, and those from vascular plants in the family Apiaceae, contain similar acidic residues but are shaped differently from those of plant plastocyanins—they lack residues 57 and 58. In cyanobacteria, the distribution of charged residues on the surface is different from eukaryotic plastocyanins and variations among different bacterial species is large. Many cyanobacterial plastocyanins have 107 amino acids. Although the acidic patches are not conserved in bacteria, the hydrophobic patch is always present. These hydrophobic and acidic patches are believed to be the recognition/binding sites for the other proteins involved in electron transfer.
Plastocyanin (Cu2+Pc) is reduced (an electron is added) by cytochrome f according to the following reaction:
After dissociation, Cu+Pc diffuses through the lumen space until recognition/binding occurs with P700+, at which point P700+ oxidizes Cu+Pc according to the following reaction:
The redox potential is about 370 mV [6] and the isoelectric pH is about 4. [7]
A catalyst's function is to increase the speed of the electron transfer (redox) reaction. Plastocyanin is believed to work less like an enzyme where enzymes decrease the transition energy needed to transfer the electron. Plastocyanin works more on the principles of entatic states where it increases the energy of the reactants, decreasing the amount of energy needed for the redox reaction to occur. Another way to rephrase the function of plastocyanin is that it can facilitate the electron transfer reaction by providing a small reorganization energy, which has been measured to about 16–28 kcal/mol (67–117 kJ/mol). [8]
To study the properties of the redox reaction of plastocyanin, methods such as quantum mechanics / molecular mechanics (QM/MM) molecular dynamics simulations. This method was used to determine that plastocyanin has an entatic strain energy of about 10 kcal/mol (42 kJ/mol). [8]
Four-coordinate copper complexes often exhibit square planar geometry, however plastocyanin has a trigonally distorted tetrahedral geometry. This distorted geometry is less stable than ideal tetrahedral geometry due to its lower ligand field stabilization as a result of the trigonal distortion. This unusual geometry is induced by the rigid “pre-organized” conformation of the ligand donors by the protein, which is an entatic state. Plastocyanin performs electron transfer with the redox between Cu(I) and Cu(II), and it was first theorized that its entatic state was a result of the protein imposing an undistorted tetrahedral geometry preferred by ordinary Cu(I) complexes onto the oxidized Cu(II) site. [10] However, a highly distorted tetrahedral geometry is induced upon the oxidized Cu(II) site instead of a perfectly symmetric tetrahedral geometry. A feature of the entatic state is a protein environment that is capable of preventing ligand dissociation even at a high enough temperature to break the metal-ligand bond. In the case of plastocyanin, it has been experimentally determined through absorption spectroscopy that there is a long and weak Cu(I)-SMet bond that should dissociate at physiological temperature due to increased entropy. However, this bond does not dissociate due to the constraints of the protein environment dominating over the entropic forces. [11]
In ordinary copper complexes involved in Cu(I)/Cu(II) redox coupling without a constraining protein environment, their ligand geometry changes significantly, and typically corresponds to the presence of a Jahn-Teller distorting force. However, the Jahn-Teller distorting force is not present in plastocyanin due to a large splitting of the dx2-y2 and dxy orbitals (See Blue Copper Protein Entatic State). Additionally, the structure of plastocyanin exhibits a long Cu(I)-SMet bond (2.9Å) with decreased electron donation strength. This bond also shortens the Cu(I)-SCys bond (2.1Å), increasing its electron donating strength. Overall, plastocyanin exhibits a lower reorganization energy due to the entatic state of the protein ligand enforcing the same distorted tetrahedral geometry in both the Cu(II) and Cu(I) oxidation states, enabling it to perform electron transfer at a faster rate. [13] The reorganization energy of blue copper proteins such as plastocyanin from 0.7 to 1.2 eV (68-116 kJ/mol) compared to 2.4 eV (232 kJ/mol) in an ordinary copper complex such as [Cu(phen)2]2+/+. [10]
Usually, plastocyanin can be found in organisms that contain chlorophyll b and cyanobacteria, as well as algae that contain chlorophyll c. Plastocyanin has also been found in the diatom, Thalassiosira oceanica, which can be found in oceanic environments. It was surprising to find these organisms containing the protein plastocyanin because the concentration of copper dissolved in the ocean is usually low (between 0.4 – 50 nM). However, the concentration of copper in the oceans is comparatively higher compared to the concentrations of other metals such as zinc and iron. Other organisms that live in the ocean, such as other phytoplankton species, have adapted to where they do not need as high of concentrations of these low concentration metals (Fe and Zn) to facilitate photosynthesis and grow. [14]
Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than alternative fermentation processes such as anaerobic glycolysis.
Metalloprotein is a generic term for a protein that contains a metal ion cofactor. A large proportion of all proteins are part of this category. For instance, at least 1000 human proteins contain zinc-binding protein domains although there may be up to 3000 human zinc metalloproteins.
In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction. It usually consists of three to four amino acids, while other amino acids within the protein are required to maintain the tertiary structure of the enzymes.
Photosystem I is one of two photosystems in the photosynthetic light reactions of algae, plants, and cyanobacteria. Photosystem I is an integral membrane protein complex that uses light energy to catalyze the transfer of electrons across the thylakoid membrane from plastocyanin to ferredoxin. Ultimately, the electrons that are transferred by Photosystem I are used to produce the moderate-energy hydrogen carrier NADPH. The photon energy absorbed by Photosystem I also produces a proton-motive force that is used to generate ATP. PSI is composed of more than 110 cofactors, significantly more than Photosystem II.
Iron–sulfur proteins are proteins characterized by the presence of iron–sulfur clusters containing sulfide-linked di-, tri-, and tetrairon centers in variable oxidation states. Iron–sulfur clusters are found in a variety of metalloproteins, such as the ferredoxins, as well as NADH dehydrogenase, hydrogenases, coenzyme Q – cytochrome c reductase, succinate – coenzyme Q reductase and nitrogenase. Iron–sulfur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe–S clusters. They have many other functions including catalysis as illustrated by aconitase, generation of radicals as illustrated by SAM-dependent enzymes, and as sulfur donors in the biosynthesis of lipoic acid and biotin. Additionally, some Fe–S proteins regulate gene expression. Fe–S proteins are vulnerable to attack by biogenic nitric oxide, forming dinitrosyl iron complexes. In most Fe–S proteins, the terminal ligands on Fe are thiolate, but exceptions exist.
The cytochrome b6f complex (plastoquinol/plastocyanin reductase or plastoquinol/plastocyanin oxidoreductase; EC 7.1.1.6) is an enzyme found in the thylakoid membrane in chloroplasts of plants, cyanobacteria, and green algae, that catalyzes the transfer of electrons from plastoquinol to plastocyanin:
A photosynthetic reaction center is a complex of several proteins, pigments, and other co-factors that together execute the primary energy conversion reactions of photosynthesis. Molecular excitations, either originating directly from sunlight or transferred as excitation energy via light-harvesting antenna systems, give rise to electron transfer reactions along the path of a series of protein-bound co-factors. These co-factors are light-absorbing molecules (also named chromophores or pigments) such as chlorophyll and pheophytin, as well as quinones. The energy of the photon is used to excite an electron of a pigment. The free energy created is then used, via a chain of nearby electron acceptors, for a transfer of hydrogen atoms (as protons and electrons) from H2O or hydrogen sulfide towards carbon dioxide, eventually producing glucose. These electron transfer steps ultimately result in the conversion of the energy of photons to chemical energy.
Rubredoxins are a class of low-molecular-weight iron-containing proteins found in sulfur-metabolizing bacteria and archaea. Sometimes rubredoxins are classified as iron-sulfur proteins; however, in contrast to iron-sulfur proteins, rubredoxins do not contain inorganic sulfide. Like cytochromes, ferredoxins and Rieske proteins, rubredoxins are thought to participate in electron transfer in biological systems. Recent work in bacteria and algae have led to the hypothesis that some rubredoxins may instead have a role in delivering iron to metalloproteins.
Cytochrome b within both molecular and cell biology, is a protein found in the membranes of aerobic cells. In eukaryotic mitochondria and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III — also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is an homologous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase, also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.
Copper proteins are proteins that contain one or more copper ions as prosthetic groups. Copper proteins are found in all forms of air-breathing life. These proteins are usually associated with electron-transfer with or without the involvement of oxygen (O2). Some organisms even use copper proteins to carry oxygen instead of iron proteins. A prominent copper protein in humans is in cytochrome c oxidase (cco). This enzyme cco mediates the controlled combustion that produces ATP. Other copper proteins include some superoxide dismutases used in defense against free radicals, peptidyl-α-monooxygenase for the production of hormones, and tyrosinase, which affects skin pigmentation.
Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.
P700, or photosystem I primary donor, is the reaction-center chlorophyll a molecular dimer associated with photosystem I in plants, algae, and cyanobacteria.
Stellacyanin is a member of the blue or type I copper protein family. This family of copper proteins is generally involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Stellacyanin is ubiquitous among vascular seed plants.
Plastocyanin/azurin family of copper-binding proteins is a family of small proteins that bind a single copper atom and that are characterised by an intense electronic absorption band near 600 nm. The most well-known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings; cusacyanin from cucumber; halocyanin from Natronomonas pharaonis, a membrane-associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans; stellacyanin from Rhus vernicifera ; umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein has evolutary relation to the above proteins, but seems to have lost the ability to bind copper. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved.
Azurin is a small, periplasmic, bacterial blue copper protein found in Pseudomonas, Bordetella, or Alcaligenes bacteria. Azurin moderates single-electron transfer between enzymes associated with the cytochrome chain by undergoing oxidation-reduction between Cu(I) and Cu(II). Each monomer of an azurin tetramer has a molecular weight of approximately 14kDa, contains a single copper atom, is intensively blue, and has a fluorescence emission band centered at 308 nm.
In bioinorganic chemistry, an entatic state is "a state of an atom or group which, due to its binding in a protein, has its geometric or electronic condition adapted for function." The term was coined by Bert Vallee and R. J. P. Williams, following work on the catalytic activity of carbonic anhydrase. These states are thought to enhance the chemistry of metal ions in biological catalysis.
Light-dependent reactions are certain photochemical reactions involved in photosynthesis, the main process by which plants acquire energy. There are two light dependent reactions: the first occurs at photosystem II (PSII) and the second occurs at photosystem I (PSI).
Transition metal thiolate complexes are metal complexes containing thiolate ligands. Thiolates are ligands that can be classified as soft Lewis bases. Therefore, thiolate ligands coordinate most strongly to metals that behave as soft Lewis acids as opposed to those that behave as hard Lewis acids. Most complexes contain other ligands in addition to thiolate, but many homoleptic complexes are known with only thiolate ligands. The amino acid cysteine has a thiol functional group, consequently many cofactors in proteins and enzymes feature cysteinate-metal cofactors.
Galactose oxidase is an enzyme that catalyzes the oxidation of D-galactose in some species of fungi.
Nickel superoxide dismutase (Ni-SOD) is a metalloenzyme that, like the other superoxide dismutases, protects cells from oxidative damage by catalyzing the disproportionation of the cytotoxic superoxide radical to hydrogen peroxide and molecular oxygen. Superoxide is a reactive oxygen species that is produced in large amounts during photosynthesis and aerobic cellular respiration. The equation for the disproportionation of superoxide is shown below: