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DNA Photolyase N-terminal Domain
DNA photolyase, N-terminal is an evolutionary conserved protein domain. This domain binds a light harvesting chromophore that enhanced the spectrum of photolyase or cryptochrome light absorption, i.e. an antenna. It adopts the rossmann fold. The cofactor may be either the pterin 5,10-Methenyltetrahydrofolate (MTHF, ) in ''folate photolyases'' () or the deazaflavin 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF, ) in ''deazaflavin photolyases'' (). The 8-HDF ligand usually binds into this domain (next to the C-terinal half), while MHF tends to bind to an outside groove of this domain. A structural signature for 8-HDF binding has been produced, highlighting amino acid residues that determine which antenna a photolyase can use. Experiments on a ''Thermus thermophilus'' protein with this domain () shows that artificial substrates can be alternatively used for a modified absorption spectra. It naturally binds FMN in a pose similar to 8-HDF. In addition, many cryptochromes, especia ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer aft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromophore
A chromophore is the part of a molecule responsible for its color. The color that is seen by our eyes is the one not absorbed by the reflecting object within a certain wavelength spectrum of visible light. The chromophore is a region in the molecule where the energy difference between two separate molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state. In biological molecules that serve to capture or detect light energy, the chromophore is the moiety that causes a conformational change in the molecule when hit by light. Conjugated pi-bond system chromophores Just like how two adjacent p-orbitals in a molecule will form a pi-bond, three or more adjacent p-orbitals in a molecule can form a conjugated pi-system. In a conjugated pi-system, electrons are able to capture certain photons as the electrons resonate along a certain distance ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Photolyase
Photolyases () are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. These enzymes require visible light (from the violet/blue end of the spectrum) both for their own activation and for the actual DNA repair. The DNA repair mechanism involving photolyases is called photoreactivation. They mainly convert pyrimidine dimers into a normal pair of pyrimidine bases. Function Photolyases bind complementary DNA strands and break certain types of pyrimidine dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA become covalently linked. The bond length of this dimerization is shorter than the bond length of normal B-DNA structure which produces an incorrect template for replication and transcription. The more common covalent linkage involves the formation of a cyclobutane bridge. Photolyases have a high affinity for these lesions and reversibly bind and convert them back to the original bases. Evolution Photolyase is a ph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryptochrome
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields in a number of species. The name ''cryptochrome'' was proposed as a ''portmanteau'' combining the '' chromatic'' nature of the photoreceptor, and the ''cryptogamic'' organisms on which many blue-light studies were carried out. The two genes ''Cry1'' and ''Cry2'' code the two cryptochrome proteins CRY1 and CRY2. In insects and plants, CRY1 regulates the circadian clock in a light-dependent fashion, whereas in mammals, CRY1 and CRY2 act as light-independent inhibitors of CLOCK-BMAL1 components of the circadian clock. In plants, blue-light photoreception can be used to cue developmental signals. Besides chlorophylls, cryptochromes are the only proteins known to form photoinduced radical-pairs ''in vivo''. These appear to enable some animal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rossmann Fold
The Rossmann fold is a tertiary fold found in proteins that bind nucleotides, such as enzyme cofactors FAD, NAD+, and NADP+. This fold is composed of alternating beta strands and alpha helical segments where the beta strands are hydrogen bonded to each other forming an extended beta sheet and the alpha helices surround both faces of the sheet to produce a three-layered sandwich. The classical Rossmann fold contains six beta strands whereas Rossmann-like folds, sometimes referred to as Rossmannoid folds, contain only five strands. The initial beta-alpha-beta (bab) fold is the most conserved segment of the Rossmann fold. The motif is named after Michael Rossmann who first noticed this structural motif in the enzyme lactate dehydrogenase in 1970 and who later observed that this was a frequently occurring motif in nucleotide binding proteins. Rossmann and Rossmannoid fold proteins are extremely common. They make up 20% of proteins with known structures in the Protein Data Bank, and a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pterin
Pterin is a heterocyclic compound composed of a pteridine ring system, with a "keto group" (a lactam) and an amino group on positions 4 and 2 respectively. It is structurally related to the parent bicyclic heterocycle called pteridine. Pterins, as a group, are compounds related to pterin with additional substituents. Pterin itself is of no biological significance. Pterins were first discovered in the pigments of butterfly wings (hence the origin of their name, from the Greek ''pteron (πτερόν)'', wing) and perform many roles in coloration in the biological world. Chemistry Pterins exhibit a wide range of tautomerism in water, beyond what is assumed by just keto-enol tautomerism. For the unsubstituted pterin, at least five tautomers are commonly cited. For 6-methylpterin, seven tautomers are theoretically predicted to be important in solution. The pteridine ring system contains four nitrogen atoms, reducing its aromaticity to the point that it can be attacked by nucleo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5,10-Methenyltetrahydrofolate
5,10-Methenyltetrahydrofolate (5,10-CH=THF) is a form of tetrahydrofolate that is an intermediate in metabolism. 5,10-CH=THF is a coenzyme that accepts and donates methenyl (CH=) groups. It is produced from 5,10-methylenetetrahydrofolate by either a NAD+ dependent methylenetetrahydrofolate dehydrogenase, or a NADP+ dependent dehydrogenase. It can also be produced as an intermediate in histidine catabolism, by formiminotransferase cyclodeaminase, from 5-formiminotetrahydrofolate. 5,10-CH=THF is a substrate for methenyltetrahydrofolate cyclohydrolase In enzymology, a methenyltetrahydrofolate cyclohydrolase () is an enzyme that catalyzes the chemical reaction :5,10-methenyltetrahydrofolate + H2O \rightleftharpoons 10-formyltetrahydrofolate Thus, the two substrates of this enzyme are 5,10-met ..., which converts it into 10-formyltetrahydrofolate. Interactive pathway map References {{DEFAULTSORT:Methenyltetrahydrofolate, 5,10- Folates Coenzymes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Deazaflavin
Coenzyme F420 or 8-hydroxy-5-deazaflavin is a coenzyme (sometimes called a cofactor) involved in redox reactions in methanogens, in many Actinomycetota, and sporadically in other bacterial lineages. It is a flavin derivative. The coenzyme is a substrate for coenzyme F420 hydrogenase, 5,10-methylenetetrahydromethanopterin reductase and methylenetetrahydromethanopterin dehydrogenase. A particularly rich natural source of F420 is ''Mycobacterium smegmatis'', in which several dozen enzymes use F420 instead of the related cofactor FMN used by homologous enzymes in most other species. Eukaryotes including the fruit fly ''Drosophila melanogaster'' and the algae ''Ostreococcus tauri'' also use a precursor to this cofactor. Biosynthesis Coenzyme F420 is synthesized via a multi-step pathway: * 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase produces Coenzyme FO (also written F0), itself a cofactor of DNA photolyase (antenna). This is the head portion of the molecule. * 2-phos ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Flavin Mononucleotide
Flavin mononucleotide (FMN), or riboflavin-5′-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as the prosthetic group of various oxidoreductases, including NADH dehydrogenase, as well as cofactor in biological blue-light photo receptors. During the catalytic cycle, a reversible interconversion of the oxidized (FMN), semiquinone (FMNH•), and reduced (FMNH2) forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than NAD and is particularly useful because it can take part in both one- and two-electron transfers. In its role as blue-light photo receptor, (oxidized) FMN stands out from the 'conventional' photo receptors as the signaling state and not an E/Z isomerization. It is the principal form in which riboflavin is found in cells and tissues. It requires more energy to produce, but is more soluble than riboflavin. In cells, FMN occurs freely circulating but also in several covalently b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CRY1
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields in a number of species. The name ''cryptochrome'' was proposed as a '' portmanteau'' combining the ''chromatic'' nature of the photoreceptor, and the '' cryptogamic'' organisms on which many blue-light studies were carried out. The two genes ''Cry1'' and ''Cry2'' code the two cryptochrome proteins CRY1 and CRY2. In insects and plants, CRY1 regulates the circadian clock in a light-dependent fashion, whereas in mammals, CRY1 and CRY2 act as light-independent inhibitors of CLOCK- BMAL1 components of the circadian clock. In plants, blue-light photoreception can be used to cue developmental signals. Besides chlorophylls, cryptochromes are the only proteins known to form photoinduced radical-pairs '' in vivo''. These appear to enable s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CRY2
Cryptochromes (from the Greek κρυπτός χρώμα, "hidden colour") are a class of flavoproteins found in plants and animals that are sensitive to blue light. They are involved in the circadian rhythms and the sensing of magnetic fields in a number of species. The name ''cryptochrome'' was proposed as a ''portmanteau'' combining the ''chromatic'' nature of the photoreceptor, and the ''cryptogamic'' organisms on which many blue-light studies were carried out. The two genes ''Cry1'' and ''Cry2'' code the two cryptochrome proteins CRY1 and CRY2. In insects and plants, CRY1 regulates the circadian clock in a light-dependent fashion, whereas in mammals, CRY1 and CRY2 act as light-independent inhibitors of CLOCK-BMAL1 components of the circadian clock. In plants, blue-light photoreception can be used to cue developmental signals. Besides chlorophylls, cryptochromes are the only proteins known to form photoinduced radical-pairs ''in vivo''. These appear to enable some animals ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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