Sandbox122: Difference between revisions
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[[Image:1G28.pdb b.jpg | thumb]] | [[Image:1G28.pdb b.jpg | thumb]] | ||
'''STRUCTURE OF A FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/PHOTOTROPIN PHOTORECEPTOR PHY3'''{{STRUCTURE_1g28| PDB=1g28 | SCENE= }} | |||
'''Phototropin''' is a blue light receptor involved in the phototropism (it is a phenomenon which is growth directed by light).This is a transmembrane protein present on the top of coleoptile. | '''Phototropin''' is a blue light receptor involved in the phototropism (it is a phenomenon which is growth directed by light).This is a transmembrane protein present on the top of coleoptile. | ||
This protein is a dimer (phot1 and phot2) and each subunit contains three domains : LOV1, '''LOV2''' (light,oxygen or voltage) domains and a kinase domain. | This protein is a dimer (phot1 and phot2) and each subunit contains three domains : LOV1, '''LOV2''' (light,oxygen or voltage) domains and a kinase domain. | ||
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==Structure of LOV2== | ==Structure of LOV2== | ||
The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical | The structure of a flaving domain, LOV2, from the chimeric phototropin photoreceptor PHY3, has been determined thanks to X-Ray diffraction. This domain is composed by four chains which are identical and called A, B, C and D. It's a L-polypeptide which weight is 50552,99 Da. Each chains has 104 aminoacids and possess four <scene name='Sandbox122/Helix_of_the_lov2_domain/1'>helix</scene> (28 residues which represents 26%) and six B <scene name='Sandbox122/Beta_sheets_of_lov2/1'>sheets</scene> (37 residues which represent 35%). | ||
==Interaction between FMN et LOV2 domain== | ==Interaction between FMN et LOV2 domain== | ||
The <scene name='Sandbox122/Fmn_ligand/1'>FMN</scene> (Flavin MonoNucleotide) is the ligand which is responsible for the light absorption. A single molecule of FMN is bound non convalently in the interior of LOV2 domain. FMN is stabilized thanks to hydrogen bonds, Van der Waals and electrostatic interactions. For example, atoms <scene name='Sandbox122/Arg_983/1'>R983</scene> and <scene name='Sandbox122/Arg_963/1'>R967</scene>(alpha C helix) create ionic bond with phosphate group of FMN. <scene name='Sandbox122/Q970/1'>Q970</scene>, <scene name='Sandbox122/N965/1'>N965</scene> , <scene name='Sandbox122/N998/1'>N988</scene>, <scene name='Sandbox122/N1008/1'>N1008</scene> (alpha A helix and beta-strand C, D and E) aminoacid make some electrostatic interaction which stabilize FMN. Some results indicate that the majority of the FMN in the LOV2 domain exist in the protonated form. Researcher propose a reaction mechanism that involves excited-state proton transfer, on the nanosecond time scale , from the sulfhydryl group of the conserved cysteine to the N5 atom of FMN. | The <scene name='Sandbox122/Fmn_ligand/1'>FMN</scene> (Flavin MonoNucleotide) is the ligand which is responsible for the light absorption. A single molecule of FMN is bound non convalently in the interior of LOV2 domain. FMN is stabilized thanks to hydrogen bonds, Van der Waals and electrostatic interactions. For example, atoms <scene name='Sandbox122/Arg_983/1'>R983</scene> and <scene name='Sandbox122/Arg_963/1'>R967</scene>(alpha C helix) create ionic bond with phosphate group of FMN. <scene name='Sandbox122/Q970/1'>Q970</scene>, <scene name='Sandbox122/N965/1'>N965</scene> , <scene name='Sandbox122/N998/1'>N988</scene>, <scene name='Sandbox122/N1008/1'>N1008</scene> (alpha A helix and beta-strand C, D and E) aminoacid make some electrostatic interaction which stabilize FMN. Some results indicate that the majority of the FMN in the LOV2 domain exist in the protonated form. Researcher propose a reaction mechanism that involves excited-state proton transfer, on the nanosecond time scale , from the sulfhydryl group of the conserved cysteine to the N5 atom of FMN. | ||
Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of Cys966. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme). | Blue light arrives on the only LOV2 <scene name='Sandbox122/Cystein_residue/1'>cystein residue</scene>(situate 4.2A from atom C(4a)) and induces formation of covalent cysteinyl-C(4a)adduct. (To explain that, refer to the scheme). Somes studies showed that temperature have an influence on that adduct. In fact, at low temperature, the microenvironment determine the reactivity of the S-H group of <scene name='Sandbox122/Cys966/2'>Cys966</scene>. A base-catalyzed mechanism for dark state recovery. Imidazole snatch proton from N5 atom of FMN and give it to the cysteine again (explain on the scheme). | ||
[[Image:Noname05.gif | thumb]] | [[Image:Noname05.gif | thumb]] | ||
