Sandbox Reserved 951: Difference between revisions

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====Interactions with ligands====

The active site is not strictly highlighted according to the actual state of studies but some residues and motifs strongly modified have been determined and this conformation enables to find the active site. Many of these conserved residue are located on the core of the β-barrel and on the small C-terminal domain and in the surface of the N-terminal domain, which forms a <scene name='60/604470/Depression_c-ter_and_n-ter/1'>depression</scene>. However, this depression is too large to enable interactions between residues and substrates, so it is thought that a conformational change occurs and sandwiches the substrates, forming the active site. This conformational change provide a suitable environment for light production because of water molecules will be excluded from the active site, favouring intramolecular reactions. Residues also follow a <scene name='60/604470/Cleft/1'>cleft</scene> caused by of the <scene name='60/604470/Beta_sheet_b/3'>Beta-sheet B</scene> against the <scene name='60/604470/Beta_barrel/3'>Beta-barrel</scene>.<ref>PMID:8805533</ref>

The active site is not strictly highlighted according to the actual state of studies but some residues and motifs strongly modified have been determined and this conformation enables to find the active site. Many of these conserved residue are located on the core of the β-barrel and on the small C-terminal domain and in the surface of the N-terminal domain, which forms a <scene name='60/604470/Depression_c-ter_and_n-ter/1'>depression</scene>. However, this depression is too large to enable interactions between residues and substrates, so it is thought that a conformational change occurs and sandwiches the substrates, forming the active site. This conformational change provide a suitable environment for light production because of water molecules will be excluded from the active site, favouring intramolecular reactions. Residues also follow a <scene name='60/604470/Cleft/1'>cleft</scene> caused by of the <scene name='60/604470/Beta_sheet_b/3'>Beta-sheet B</scene> against the <scene name='60/604470/Beta_barrel/3'>Beta-barrel</scene>.<ref name =''fourth'>PMID:8805533</ref>

[[Image:Luciferin_bounding_to_luciferase.jpg|250px|right|thumb|Hydrogen bonding between Luciferase and substrates luciferin (green), ATP (violet) and Mg2+,<ref>[http://www.photobiology.info/ Photobiology]</ref>]]

=====Interaction with ATP=====

We find a signal motif in luciferase which is <scene name='60/604470/Atp_binding_signal_motif/1'>[STG]-[STG]-G-[ST]-[ST]-[TSE]-[GS]-x-[PALIVM]-K</scene> where some residue like lysine are always conserved. This pattern enables ATP binding thanks to hydrogen bonds between residues and phosphates of ATP. There is another pattern : <scene name='60/604470/Adenosine_ring_binding/1'>[YFW]-[GASW]-x-[TSA]-E</scene> which takes a particular conformation because of hydrogen bonds between residues and maintain the adenosin ring of ATP.<ref>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>

We find a signal motif in luciferase which is <scene name='60/604470/Atp_binding_signal_motif/1'>[STG]-[STG]-G-[ST]-[ST]-[TSE]-[GS]-x-[PALIVM]-K</scene> where some residue like lysine are always conserved. This pattern enables ATP binding thanks to hydrogen bonds between residues and phosphates of ATP. There is another pattern : <scene name='60/604470/Adenosine_ring_binding/1'>[YFW]-[GASW]-x-[TSA]-E</scene> which takes a particular conformation because of hydrogen bonds between residues and maintain the adenosin ring of ATP.<ref name =''fifth''>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>

=====Interaction with luciferin=====

Luciferase holds the luciferin with the specific residues <scene name='60/604470/Residues_helding_luciferin/1'>arginin 218, phenylalanin 247, serin 347 and adenin 348</scene>, still with hydrogen bounds. This bindings makes the carboxylate oxygen of luciferin points toward the α phosphate of ATP, so the oxygen is well-positionned to attack the α phosphate. This promotes the luciferin-AMP formation.<ref>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>

Sandbox Reserved 951: Difference between revisions

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@@ Line 32: / Line 32: @@
 ====Interactions with ligands====
-The active site is not strictly highlighted according to the actual state of studies but some residues and motifs strongly modified have been determined and this conformation enables to find the active site. Many of these conserved residue are located on the core of the β-barrel and on the small C-terminal domain and in the surface of the N-terminal domain, which forms a <scene name='60/604470/Depression_c-ter_and_n-ter/1'>depression</scene>. However, this depression is too large to enable interactions between residues and substrates, so it is thought that a conformational change occurs and sandwiches the substrates, forming the active site. This conformational change provide a suitable environment for light production because of water molecules will be excluded from the active site, favouring intramolecular reactions. Residues also follow a <scene name='60/604470/Cleft/1'>cleft</scene> caused by of the <scene name='60/604470/Beta_sheet_b/3'>Beta-sheet B</scene> against the <scene name='60/604470/Beta_barrel/3'>Beta-barrel</scene>.<ref>PMID:8805533</ref>
+The active site is not strictly highlighted according to the actual state of studies but some residues and motifs strongly modified have been determined and this conformation enables to find the active site. Many of these conserved residue are located on the core of the β-barrel and on the small C-terminal domain and in the surface of the N-terminal domain, which forms a <scene name='60/604470/Depression_c-ter_and_n-ter/1'>depression</scene>. However, this depression is too large to enable interactions between residues and substrates, so it is thought that a conformational change occurs and sandwiches the substrates, forming the active site. This conformational change provide a suitable environment for light production because of water molecules will be excluded from the active site, favouring intramolecular reactions. Residues also follow a <scene name='60/604470/Cleft/1'>cleft</scene> caused by of the <scene name='60/604470/Beta_sheet_b/3'>Beta-sheet B</scene> against the <scene name='60/604470/Beta_barrel/3'>Beta-barrel</scene>.<ref name =''fourth'>PMID:8805533</ref>
 [[Image:Luciferin_bounding_to_luciferase.jpg|250px|right|thumb|Hydrogen bonding between Luciferase and substrates luciferin (green), ATP (violet) and Mg2+,<ref>[http://www.photobiology.info/ Photobiology]</ref>]]
 =====Interaction with ATP=====
-We find a signal motif in luciferase which is <scene name='60/604470/Atp_binding_signal_motif/1'>[STG]-[STG]-G-[ST]-[ST]-[TSE]-[GS]-x-[PALIVM]-K</scene> where some residue like lysine are always conserved. This pattern enables ATP binding thanks to hydrogen bonds between residues and phosphates of ATP. There is another pattern : <scene name='60/604470/Adenosine_ring_binding/1'>[YFW]-[GASW]-x-[TSA]-E</scene> which takes a particular conformation because of hydrogen bonds between residues and maintain the adenosin ring of ATP.<ref>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>
+We find a signal motif in luciferase which is <scene name='60/604470/Atp_binding_signal_motif/1'>[STG]-[STG]-G-[ST]-[ST]-[TSE]-[GS]-x-[PALIVM]-K</scene> where some residue like lysine are always conserved. This pattern enables ATP binding thanks to hydrogen bonds between residues and phosphates of ATP. There is another pattern : <scene name='60/604470/Adenosine_ring_binding/1'>[YFW]-[GASW]-x-[TSA]-E</scene> which takes a particular conformation because of hydrogen bonds between residues and maintain the adenosin ring of ATP.<ref name =''fifth''>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>
 =====Interaction with luciferin=====
 Luciferase holds the luciferin with the specific residues <scene name='60/604470/Residues_helding_luciferin/1'>arginin 218, phenylalanin 247, serin 347 and adenin 348</scene>, still with hydrogen bounds. This bindings makes the carboxylate oxygen of luciferin points toward the α phosphate of ATP, so the oxygen is well-positionned to attack the α phosphate. This promotes the luciferin-AMP formation.<ref>PMID:8805533</ref>, <ref>[http://www.photobiology.info/ Photobiology]</ref>