User:Matt Whelihan: Difference between revisions

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[[Image:luciferase.jpg]]

== '''Firefly Luciferase''' ==

Bioluminescence is the process by which living organisms convert chemical energy into photons of light and it is widely distributed throughout the animals, plants and fungi <ref>PMID:6358519</ref>. Species use bioluminescence as a survival tool in mating, defense and hunting. The one thing that all bioluminescent species have in common is that they all catalyze the reaction with an enzyme generically called a luciferase. All luciferases oxidize a substrate, which then decays back to the ground state while emitting a photon of light. This process is incredibly efficient with almost one photon of light produced per oxidation. While all lucifeases oxidize their substrates, the cofactors involved and reaction pathways used, vary widely <ref>PMID:775940</ref><ref>PMID:14444706</ref>.

----

One of the most studied of all luciferases is that of the <scene name='User:Matt_Whelihan/Rainbow_n-c/1'>Firefly</scene>. This particular luciferase enzyme is located in the light emitting organ known as the lantern in the abdomen of the beetle. Firefly larvae glow green to ward off predators and adult fireflies use this mechanism of bioluminescence to attract mates. Luciferase binds ATP/Mg+ and D-luciferin and oxidizes it to Oxyluciferin with the products of one photon of yellow-green light, pyrophosphate, AMP and CO2<ref>PMID:775940</ref>. The crystal structures of two firefly luciferases, the North American Firefly (''Photinus pyralis'')<ref>PMID:8805533</ref> and the Japanese Firefly (''Luciola cruciata'')<ref>PMID:16541080</ref> 16541080 have been solved.

One of the most studied of all luciferases is that of the <scene name='User:Matt_Whelihan/Rainbow_n-c/1'>Firefly</scene>. This particular luciferase enzyme is located in the light emitting organ known as the lantern in the abdomen of the beetle. Firefly larvae glow green to ward off predators and adult fireflies use this mechanism of bioluminescence to attract mates. Luciferase binds ATP/Mg+ and D-luciferin and oxidizes it to Oxyluciferin with the products of one photon of yellow-green light, pyrophosphate, AMP and CO2<ref>PMID:775940</ref>. The crystal structures of two firefly luciferases, the North American Firefly (''Photinus pyralis'') <ref>PMID:8805533</ref> and the Japanese Firefly (''Luciola cruciata'')<ref>PMID:16541080</ref> 16541080 have been solved.

Both the Japanese and North American luciferase variants are single-chain 62 kDa monooxygenases with two distinct domains. ~~The luciferase~~ <scene name='User:Matt_Whelihan/Secondary_structure/1'>~~structure~~</scene> ~~from ''L. cruciata'' is~~ comprised of a mix of alpha and beta secondary structures that form four distinct motifs. The <scene name='User:Matt_Whelihan/N-terminal_domain/1'>N-terminal domain</scene> (residues 4-436) is comprised of of an antiparalell β-barrel and two β-sheets, flanked by α-helices which forms a typical Rossmann fold [http://images.google.com/imgres?imgurl=http://chem.csusb.edu/~dpedersn/C436/openbetarossman.jpg&imgrefurl=http://chem.csusb.edu/~dpedersn/C436/prot_struct_and_class.html&usg=__xOF4ifmAyJ5qm3UPaNKd9whKlu4=&h=539&w=719&sz=35&hl=en&start=5&um=1&tbnid=IMkWKmy0xzWcYM:&tbnh=105&tbnw=140&prev=/images%3Fq%3DRossman%2BFold%26hl%3Den%26safe%3Doff%26sa%3DN%26um%3D1] The

Both the Japanese and North American luciferase variants are single-chain 62 kDa monooxygenases with two distinct domains. Their <scene name='User:Matt_Whelihan/Secondary_structure/1'>structures</scene> are comprised of a mix of alpha and beta secondary structures that form four distinct motifs. The <scene name='User:Matt_Whelihan/N-terminal_domain/1'>N-terminal domain</scene> (residues 4-436) is comprised of of an antiparalell β-barrel and two β-sheets, flanked by α-helices which forms a typical Rossmann fold [http://images.google.com/imgres?imgurl=http://chem.csusb.edu/~dpedersn/C436/openbetarossman.jpg&imgrefurl=http://chem.csusb.edu/~dpedersn/C436/prot_struct_and_class.html&usg=__xOF4ifmAyJ5qm3UPaNKd9whKlu4=&h=539&w=719&sz=35&hl=en&start=5&um=1&tbnid=IMkWKmy0xzWcYM:&tbnh=105&tbnw=140&prev=/images%3Fq%3DRossman%2BFold%26hl%3Den%26safe%3Doff%26sa%3DN%26um%3D1] The

<scene name='User:Matt_Whelihan/C-terminal_domain/2C-terminal domain</scene> (residues 440-544) is comprises of a separate α-β hinge<ref>PMID:8805533</ref>. Firefly luciferases share significant sequence and mechanistic homology with peptide synthetases and acylCoA ligases. These enzymes belong to a superfamily of adenylate-forming enzymes that catalyze activation reactions between ATP and a carboxyl group of their substrates. This group of proteins shares an identifying motif (198SerSerGlySerThrGlyLeuProLysGly207) and has been termed the “acyl-adenylate/thioester-forming” enzyme family. Despite high sequence homology, there are only seven residues that are conserved across this superfamily (Gly200, Lys206, Glu344, Asp422, Arg437, Gly446, and Glu455). These residues are believed to be integral to the binding of ATP and the formation of an adenylate compound. <ref>PMID:1447981</ref>. These residues however are located across the N and C-terminal domains, which in the structure, are too far apart to produce catalysis. This suggested suggest that the crystallized form was in the resting state of the enzyme and it was hypothesized that the C-terminal domain would close in on the active site cleft upon substrate binding. This closing of the active site combined with various hydrophobic residues seen packed around the active site suggested that catalysis may occur in the absence of water.

<scene name='User:Matt_Whelihan/C-terminal_domain/2'>C-terminal domain</scene> (residues 440-544) is comprises of a separate α-β hinge<ref>PMID:8805533</ref>. Firefly luciferases share significant sequence and mechanistic homology with peptide synthetases and acylCoA ligases. These enzymes belong to a superfamily of adenylate-forming enzymes that catalyze activation reactions between ATP and a carboxyl group of their substrates. This group of proteins shares an identifying motif (198SerSerGlySerThrGlyLeuProLysGly207) and has been termed the “acyl-adenylate/thioester-forming” enzyme family. Despite high sequence homology, there are only seven residues that are conserved across this superfamily (Gly200, Lys206, Glu344, Asp422, Arg437, Gly446, and Glu455). These residues are believed to be integral to the binding of ATP and the formation of an adenylate compound. <ref>PMID:1447981</ref>. These residues however are located across the N and C-terminal domains, which in the structure, are too far apart to produce catalysis. This suggested suggest that the crystallized form was in the resting state of the enzyme and it was hypothesized that the C-terminal domain would close in on the active site cleft upon substrate binding. This closing of the active site combined with various hydrophobic residues seen packed around the active site suggested that catalysis may occur in the absence of water.

These seven highly conserved amino acids identify the

<scene name='User:Matt_Whelihan/Active_site_residues/1'>active site</scene> which is located in the large hydrophobic cleft between the two adjacent N and C-terminal domains.

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 [[Image:luciferase.jpg]]
 == '''Firefly Luciferase''' ==
 Bioluminescence is the process by which living organisms convert chemical energy into photons of light and it is widely distributed throughout the animals, plants and fungi <ref>PMID:6358519</ref>. Species use bioluminescence as a survival tool in mating, defense and hunting. The one thing that all bioluminescent species have in common is that they all catalyze the reaction with an enzyme generically called a luciferase.  All luciferases oxidize a substrate, which then decays back to the ground state while emitting a photon of light. This process is incredibly efficient with almost one photon of light produced per oxidation. While all lucifeases oxidize their substrates, the cofactors involved and reaction pathways used, vary widely <ref>PMID:775940</ref><ref>PMID:14444706</ref>.
 ----
 <applet load='2d1r' size='400' frame='true' align='left' caption='Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=OLU&sid=2D1R] and AMP [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=AMP&sid=2D1R]' />
-One of the most studied of all luciferases is that of the <scene name='User:Matt_Whelihan/Rainbow_n-c/1'>Firefly</scene>. This particular luciferase enzyme is located in the light emitting organ known as the lantern in the abdomen of the beetle. Firefly larvae glow green to ward off predators and adult fireflies use this mechanism of bioluminescence to attract mates.  Luciferase binds ATP/Mg+ and D-luciferin and oxidizes it to Oxyluciferin with the products of one photon of yellow-green light, pyrophosphate, AMP and CO2<ref>PMID:775940</ref>. The crystal structures of two firefly luciferases, the North American Firefly (''Photinus pyralis'')<ref>PMID:8805533</ref> and the Japanese Firefly (''Luciola cruciata'')<ref>PMID:16541080</ref> 16541080 have been solved.
+One of the most studied of all luciferases is that of the <scene name='User:Matt_Whelihan/Rainbow_n-c/1'>Firefly</scene>. This particular luciferase enzyme is located in the light emitting organ known as the lantern in the abdomen of the beetle. Firefly larvae glow green to ward off predators and adult fireflies use this mechanism of bioluminescence to attract mates.  Luciferase binds ATP/Mg+ and D-luciferin and oxidizes it to Oxyluciferin with the products of one photon of yellow-green light, pyrophosphate, AMP and CO2<ref>PMID:775940</ref>. The crystal structures of two firefly luciferases, the North American Firefly (''Photinus pyralis'') <ref>PMID:8805533</ref> and the Japanese Firefly (''Luciola cruciata'')<ref>PMID:16541080</ref> 16541080 have been solved.
-Both the Japanese and North American luciferase variants are single-chain 62 kDa monooxygenases with two distinct domains. The luciferase <scene name='User:Matt_Whelihan/Secondary_structure/1'>structure</scene> from ''L. cruciata'' is comprised of a mix of alpha and beta secondary structures that form four distinct motifs. The <scene name='User:Matt_Whelihan/N-terminal_domain/1'>N-terminal domain</scene> (residues 4-436) is comprised of of an antiparalell β-barrel and two β-sheets, flanked by α-helices which forms a typical Rossmann fold [http://images.google.com/imgres?imgurl=http://chem.csusb.edu/~dpedersn/C436/openbetarossman.jpg&imgrefurl=http://chem.csusb.edu/~dpedersn/C436/prot_struct_and_class.html&usg=__xOF4ifmAyJ5qm3UPaNKd9whKlu4=&h=539&w=719&sz=35&hl=en&start=5&um=1&tbnid=IMkWKmy0xzWcYM:&tbnh=105&tbnw=140&prev=/images%3Fq%3DRossman%2BFold%26hl%3Den%26safe%3Doff%26sa%3DN%26um%3D1] The
+Both the Japanese and North American luciferase variants are single-chain 62 kDa monooxygenases with two distinct domains. Their  <scene name='User:Matt_Whelihan/Secondary_structure/1'>structures</scene> are comprised of a mix of alpha and beta secondary structures that form four distinct motifs. The <scene name='User:Matt_Whelihan/N-terminal_domain/1'>N-terminal domain</scene> (residues 4-436) is comprised of of an antiparalell β-barrel and two β-sheets, flanked by α-helices which forms a typical Rossmann fold [http://images.google.com/imgres?imgurl=http://chem.csusb.edu/~dpedersn/C436/openbetarossman.jpg&imgrefurl=http://chem.csusb.edu/~dpedersn/C436/prot_struct_and_class.html&usg=__xOF4ifmAyJ5qm3UPaNKd9whKlu4=&h=539&w=719&sz=35&hl=en&start=5&um=1&tbnid=IMkWKmy0xzWcYM:&tbnh=105&tbnw=140&prev=/images%3Fq%3DRossman%2BFold%26hl%3Den%26safe%3Doff%26sa%3DN%26um%3D1] The
-<scene name='User:Matt_Whelihan/C-terminal_domain/2C-terminal domain</scene> (residues 440-544) is comprises of a separate α-β hinge<ref>PMID:8805533</ref>. Firefly luciferases share significant sequence and mechanistic homology with peptide synthetases and acylCoA ligases. These enzymes belong to a superfamily of adenylate-forming enzymes that catalyze activation reactions between ATP and a carboxyl group of their substrates. This group of proteins shares an identifying motif (198SerSerGlySerThrGlyLeuProLysGly207) and has been termed the “acyl-adenylate/thioester-forming” enzyme family. Despite high sequence homology, there are only seven residues that are conserved across this superfamily (Gly200, Lys206, Glu344, Asp422, Arg437, Gly446, and Glu455). These residues are believed to be integral to the binding of ATP and the formation of an adenylate compound. <ref>PMID:1447981</ref>. These residues however are located across the N and C-terminal domains, which in the structure, are too far apart to produce catalysis. This suggested suggest that the crystallized form was in the resting state of the enzyme and it was hypothesized that the C-terminal domain would close in on the active site cleft upon substrate binding. This closing of the active site combined with various hydrophobic residues seen packed around the active site suggested that catalysis may occur in the absence of water.
+<scene name='User:Matt_Whelihan/C-terminal_domain/2'>C-terminal domain</scene> (residues 440-544) is comprises of a separate α-β hinge<ref>PMID:8805533</ref>. Firefly luciferases share significant sequence and mechanistic homology with peptide synthetases and acylCoA ligases. These enzymes belong to a superfamily of adenylate-forming enzymes that catalyze activation reactions between ATP and a carboxyl group of their substrates. This group of proteins shares an identifying motif (198SerSerGlySerThrGlyLeuProLysGly207) and has been termed the “acyl-adenylate/thioester-forming” enzyme family. Despite high sequence homology, there are only seven residues that are conserved across this superfamily (Gly200, Lys206, Glu344, Asp422, Arg437, Gly446, and Glu455). These residues are believed to be integral to the binding of ATP and the formation of an adenylate compound. <ref>PMID:1447981</ref>. These residues however are located across the N and C-terminal domains, which in the structure, are too far apart to produce catalysis. This suggested suggest that the crystallized form was in the resting state of the enzyme and it was hypothesized that the C-terminal domain would close in on the active site cleft upon substrate binding. This closing of the active site combined with various hydrophobic residues seen packed around the active site suggested that catalysis may occur in the absence of water.
   These seven highly conserved amino acids identify the
 <scene name='User:Matt_Whelihan/Active_site_residues/1'>active site</scene> which is located in the large hydrophobic cleft between the two adjacent N and C-terminal domains.