Luciola cruciata luciferase - Revision history

Jaime Prilusky at 10:36, 10 February 2019

2019-02-10T10:36:35Z

← Older revision		Revision as of 10:36, 10 February 2019
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	<StructureSection load='2d1r' size='~~450~~' side='right' ~~SCENE=Luciola_cruciata_luciferase/Oxyluciferin_amp/2~~ caption='Structure of Luciola cruciata complexed with Oxiluciferin & AMP (PDB entry [[2d1r]])'>		<StructureSection load='2d1r' size='350' side='right' caption='Structure of Luciola cruciata complexed with Oxiluciferin and AMP (PDB entry [[2d1r]])' scene='Luciola_cruciata_luciferase/Oxyluciferin_amp/2' >
	~~[[Image:2d1r.png\|left\|200px]]~~
	[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.		[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.
	This protein is constituted of two main domains separated by a cleft.		This protein is constituted of two main domains separated by a cleft.


	==Chemical reaction==		==Chemical reaction==

	The enzyme catalyses the production of light, using two different conformation to catalyze two half-reactions (in the case of firefly Luciferase).		The enzyme catalyses the production of light, using two different conformation to catalyze two half-reactions (in the case of firefly Luciferase).

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	It can also be used to study the action of general anesthetics<ref name="ane" />, which are inhibiting it.		It can also be used to study the action of general anesthetics<ref name="ane" />, which are inhibiting it.
	The [http://en.wikipedia.org/wiki/Luciferase#Applications applications for luciferase] are very diverse.		The [http://en.wikipedia.org/wiki/Luciferase#Applications applications for luciferase] are very diverse.



	==Biology==		==Biology==
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	==3D structures of luciferase==		==3D structures of luciferase==

	[[Luciferase]]		[[Luciferase]]

Alexander Berchansky at 13:44, 14 August 2013

2013-08-14T13:44:13Z

Alexander Berchansky at 13:39, 14 August 2013

2013-08-14T13:39:17Z

← Older revision		Revision as of 13:39, 14 August 2013
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	<StructureSection load='2d1r' size='~~500~~' side='right' SCENE=Luciola_cruciata_luciferase/Oxyluciferin_amp/2 caption='Structure of Luciola cruciata complexed with Oxiluciferin & AMP (PDB entry [[2d1r]])'>		<StructureSection load='2d1r' size='450' side='right' SCENE=Luciola_cruciata_luciferase/Oxyluciferin_amp/2 caption='Structure of Luciola cruciata complexed with Oxiluciferin & AMP (PDB entry [[2d1r]])'>
	[[Image:2d1r.png\|left\|200px]]		[[Image:2d1r.png\|left\|200px]]
	[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.		[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.

Alexander Berchansky at 13:38, 14 August 2013

2013-08-14T13:38:56Z

← Older revision		Revision as of 13:38, 14 August 2013
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			<StructureSection load='2d1r' size='500' side='right' SCENE=Luciola_cruciata_luciferase/Oxyluciferin_amp/2 caption='Structure of Luciola cruciata complexed with Oxiluciferin & AMP (PDB entry [[2d1r]])'>
	[[Image:2d1r.png\|left\|200px]]		[[Image:2d1r.png\|left\|200px]]
	~~{{STRUCTURE_2d1r\| PDB=2d1r \| SCENE= }}~~


	[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.		[[Luciferase]] is a class of enzymes producing light through the process of bioluminescence. [[Luciola cruciata luciferase]], or Japanese firefly luciferase, catalyses a reaction of adenylation and then an oxydative decarboxylation, changing luciferin to oxyluciferin and thus emitting light.
	This protein is constituted of two main domains separated by a cleft.		This protein is constituted of two main domains separated by a cleft.
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	==Structure==		==Structure==
	<StructureSection load='2d1r' size='500' side='right' SCENE=Luciola_cruciata_luciferase/Oxyluciferin_amp/2 caption='Structure of Luciola cruciata complexed with Oxiluciferin & AMP (PDB entry [[2d1r]])'>2D1R is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].		2D1R is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].
	The protein is shown here bound with two products, adenosine 5'-phosphate (AMP) and oxyluciferine.		The protein is shown here bound with two products, adenosine 5'-phosphate (AMP) and oxyluciferine.

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	=== Luciferase Control ===		=== Luciferase Control ===
	As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.		As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.
			</StructureSection>
			__NOTOC__

	==3D structures of luciferase==		==3D structures of luciferase==

Michal Harel at 08:00, 12 July 2011

2011-07-12T08:00:16Z

← Older revision		Revision as of 08:00, 12 July 2011
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	=== Luciferase Control ===		=== Luciferase Control ===
	As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.		As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.

			==3D structures of luciferase==

			[[Luciferase]]

	==See Also==		==See Also==

Loïc Gazquez at 10:58, 6 December 2010

2010-12-06T10:58:27Z

← Older revision		Revision as of 10:58, 6 December 2010
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	But the firefly luciferase also have caracteristic sequences found in no other nucleotide-binding proteins, such as a motif responsible for the binding of ATP.		But the firefly luciferase also have caracteristic sequences found in no other nucleotide-binding proteins, such as a motif responsible for the binding of ATP.

	~~===Active site===~~
	~~The firefly luciferase interacts with ATP, luciferin, an Acetyl-coenzyme A (CoA ) and O<sub>2</sub>. So differents groups of residues are part of the the ligand binding.~~
	~~Those residues can be placed in the molecule by comparing the sequence of different enzymes of the same family.~~
	~~The ATP binds to a <scene name='Sandbox2442/Atp_binding/3'>G-x-x-x-x-G-K-[STG]</scene> sequence which is a very disordered version of a classical mononucleotide-binding motif. <ref>PMID:8805533</ref>~~
	~~The luciferin-binding site seems to be a depression between β sheet B and the barrel subdomain, but is not clearly visible on the structure.~~
	The CoA-binding site does not have a classical motif of adenylate forming enzyme and this luciferase is the first member of a new superfamily to be studied. The adenylate forming reaction is likely to involve a few glycine or charged residues.
	~~The others binding sites are not clearly defined yet but there are some conserved residues taking part in the binding or the catalysis:~~

	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/3'>Thr346</scene> which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.

	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/6'>Tyr340</scene>.

	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/7'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.

	All the <scene name='Sandbox2442/Active_site/5'>conserved residues</scene> are either on the surface of the two domains on the side of the cleft or on the loop connecting the two domains. But this cleft is too big to accomodate on the substrates and is seems that the two domains only come closer around the products when they are formed.

Loïc Gazquez: /* Biology */

2010-11-26T13:10:19Z

Biology

← Older revision		Revision as of 13:10, 26 November 2010
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	==Biology==		==Biology==
	The [~~http://en.wikipedia.org/wiki/Bioluminescence~~ bioluminescent] systems in the living organisms are very diverse (for example the luciferase has a different structure and catalyses a reaction in one step in the bacteria), so it is thought that they appeared separately in the course of evolution.		The [[bioluminescent]] systems in the living organisms are very diverse (for example the luciferase has a different structure and catalyses a reaction in one step in the bacteria), so it is thought that they appeared separately in the course of evolution.
	In general [http://en.wikipedia.org/wiki/Firefly fireflies] use bioluminescence to locate other individuals for mating, or to lure other species which are their preys. In the larvae, it is a warning signal for the predators, implying the presence of toxins.		In general [http://en.wikipedia.org/wiki/Firefly fireflies] use bioluminescence to locate other individuals for mating, or to lure other species which are their preys. In the larvae, it is a warning signal for the predators, implying the presence of toxins.
	Bioluminescence is thus utilized by several nocturnal japanese firely species during mate selection, with males and females illuminating equally. Several common signals appear to be used to communicate everything from "male awaiting a mate" to "female here". <ref name="main">PMID:8813052</ref> While the reaction is quite similiar to that of other bioluminescent luciferases, firefly luciferase has a unique structure in both the protein and luciferin required to produce the bioluminescence. In research, the firefly luciferase from ''Luciola cruciata'' is one of many commonly utilized for such purposes as such as sensing cellular ATP levels or visualizing the effects of a promoter sequence, among several others.		Bioluminescence is thus utilized by several nocturnal japanese firely species during mate selection, with males and females illuminating equally. Several common signals appear to be used to communicate everything from "male awaiting a mate" to "female here". <ref name="main">PMID:8813052</ref> While the reaction is quite similiar to that of other bioluminescent luciferases, firefly luciferase has a unique structure in both the protein and luciferin required to produce the bioluminescence. In research, the firefly luciferase from ''Luciola cruciata'' is one of many commonly utilized for such purposes as such as sensing cellular ATP levels or visualizing the effects of a promoter sequence, among several others.
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	=== Luciferase Control ===		=== Luciferase Control ===
	As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.		As the structure of luciferases differ between species, so does the method of control over the bioluminescent reaction. In L. polyedrum, a marine dinoflagellate responsible for some red tides, a pH-dependant mechanism at the protein level appears to be responsible for control of bioluminescence. With fireflies however, the reaction is under at least some form of nervous control, with the insect controlling flashes through the use of nitric oxide <ref name="lights">PMID:11431567 </ref>.


	==See Also==		==See Also==

Loïc Gazquez at 12:48, 26 November 2010

2010-11-26T12:48:33Z

← Older revision		Revision as of 12:48, 26 November 2010
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	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/6'>Tyr340</scene>.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/6'>Tyr340</scene>.

	* <scene name='~~Sandbox2442~~/~~Residue_ser_420~~/1'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/7'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.

	All the <scene name='Sandbox2442/Active_site/5'>conserved residues</scene> are either on the surface of the two domains on the side of the cleft or on the loop connecting the two domains. But this cleft is too big to accomodate on the substrates and is seems that the two domains only come closer around the products when they are formed.		All the <scene name='Sandbox2442/Active_site/5'>conserved residues</scene> are either on the surface of the two domains on the side of the cleft or on the loop connecting the two domains. But this cleft is too big to accomodate on the substrates and is seems that the two domains only come closer around the products when they are formed.

Loïc Gazquez at 12:43, 26 November 2010

2010-11-26T12:43:11Z

← Older revision		Revision as of 12:43, 26 November 2010
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	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/3'>Thr346</scene> which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/3'>Thr346</scene> which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.

	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/5'>Tyr340</scene>.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/6'>Tyr340</scene>.

	* <scene name='Sandbox2442/Residue_ser_420/1'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.		* <scene name='Sandbox2442/Residue_ser_420/1'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.

Loïc Gazquez at 12:39, 26 November 2010

2010-11-26T12:39:08Z

← Older revision		Revision as of 12:39, 26 November 2010
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	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/3'>Thr346</scene> which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/3'>Thr346</scene> which is the only residue with dihedral angles outside of the usual regions of the Ramachandran plot. This energetically unfavorable angles are usually in relation with residues having important functional roles.

	* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the Tyr340.		* <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/4'>Asp422</scene> is an invariant residue exposed to the solvant, and could make an hydrogen bond with the side chain of another well-conserved residue, the <scene name='Luciola_cruciata_luciferase/Whole_protein_transparent/5'>Tyr340</scene>.

	* <scene name='Sandbox2442/Residue_ser_420/1'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.		* <scene name='Sandbox2442/Residue_ser_420/1'>Ser420</scene> has an hydroxyl group able to make hydrogen bond with the Asp422 and Gly421 which are close enough.

← Older revision		Revision as of 13:44, 14 August 2013
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	2D1R is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].		2D1R is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1R OCA].
	The protein is shown here bound with two products, adenosine 5'-phosphate (AMP) and oxyluciferine.		The protein is shown here bound with two products, adenosine 5'-phosphate (AMP) and oxyluciferine.


	It weights 62 kDa and is constituted of two main domains, a large N-terminal domain and a small C-terminal domain, separated by a cleft and linked by a hinge. <scene name='Luciola_cruciata_luciferase/Nter_domain/2'>The N-ter domain</scene> (residues 1-436) is made of a β-barrel and two β-sheets, flanked by α-helices, thus forming		It weights 62 kDa and is constituted of two main domains, a large N-terminal domain and a small C-terminal domain, separated by a cleft and linked by a hinge. <scene name='Luciola_cruciata_luciferase/Nter_domain/2'>The N-ter domain</scene> (residues 1-436) is made of a β-barrel and two β-sheets, flanked by α-helices, thus forming
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	There are two conformational states, one when the enzyme is substrate-free, and the other one product-bound (whose structure is represented on this page). The transition is achieved by a 90° counterclockwise rotation of the <scene name='Luciola_cruciata_luciferase/Cter_relative_nter/1'>C-domain relative to the N-domain</scene><ref name="ane">PMID:17513367</ref>		There are two conformational states, one when the enzyme is substrate-free, and the other one product-bound (whose structure is represented on this page). The transition is achieved by a 90° counterclockwise rotation of the <scene name='Luciola_cruciata_luciferase/Cter_relative_nter/1'>C-domain relative to the N-domain</scene><ref name="ane">PMID:17513367</ref>



	===Sequence similarities===		===Sequence similarities===
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	But the firefly luciferase also have caracteristic sequences found in no other nucleotide-binding proteins, such as a motif responsible for the binding of ATP.		But the firefly luciferase also have caracteristic sequences found in no other nucleotide-binding proteins, such as a motif responsible for the binding of ATP.




	===Spectral difference with mutated luciferases===		===Spectral difference with mutated luciferases===

	The colour changes from the classical yellow-green colour to red with the substitution of a single amino acid, <scene name='Sandbox2442/Residue_ser_286/1'>Ser286</scene> to Asn, in the S286N mutant. The active site (and the residue Ile288) is less potent to effectue it's conformational change to the closed state, which was providing an extremely hydrophobic environment. This is then allowing an energy loss, and the product will emit lower energy light, with a wavelength moved to the red.		The colour changes from the classical yellow-green colour to red with the substitution of a single amino acid, <scene name='Sandbox2442/Residue_ser_286/1'>Ser286</scene> to Asn, in the S286N mutant. The active site (and the residue Ile288) is less potent to effectue it's conformational change to the closed state, which was providing an extremely hydrophobic environment. This is then allowing an energy loss, and the product will emit lower energy light, with a wavelength moved to the red.
	Further mutations proved that the <scene name='Sandbox2442/Ile_288/1'>amino acid residue at position 288</scene> is influencing the wavelength of the light emitted.<ref>PMID:16541080</ref>~~</StructureSection>~~		Further mutations proved that the <scene name='Sandbox2442/Ile_288/1'>amino acid residue at position 288</scene> is influencing the wavelength of the light emitted.<ref>PMID:16541080</ref>

	~~{{STRUCTURE_2d1s\| PDB=2d1s \|\|SIZE=300\| SCENE=Luciferase/2d1s/2 \|CAPTION= 2d1s, resolution 1.30Å (<scene name='Luciferase/2d1s/2'>default scene</scene>). }}~~

	=== High-energy intermediate analogue===		=== High-energy intermediate analogue===
			<scene name='Luciferase/2d1s/2'>Luciferase</scene> ([[2d1s]]).

	Generally, firefly luciferases have some similarities with Acyl-CoA ligases and some peptide synthetases despite having different cellular effects. In fixing the structure of L. cruciata luciferase, the analog of a potent aminoacyl-tRNA synthetases (DLSA) was successfuly utilized to represent a stable oxyluciferin intermediate.<ref name="structure">PMID:16541080 </ref>.<br>		Generally, firefly luciferases have some similarities with Acyl-CoA ligases and some peptide synthetases despite having different cellular effects. In fixing the structure of L. cruciata luciferase, the analog of a potent aminoacyl-tRNA synthetases (DLSA) was successfuly utilized to represent a stable oxyluciferin intermediate.<ref name="structure">PMID:16541080 </ref>.<br>
	{{Link Toggle FancyCartoonHighQualityView}} on 2d1s (see right image).<br>		{{Link Toggle FancyCartoonHighQualityView}} on 2d1s (see right image).<br>