[[Image:2d1r.png|left|200px]]


{{STRUCTURE_2d1r| PDB=2d1r | SCENE= }}

=Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP=

==Introduction==

Luciferase is a class of enzymes producing light through the process of bioluminescence. This luciferase was extracted from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. In the case of fireflies, it 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.

==The structure==
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.

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. <scene name='Sandbox2442/N-ter_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
<scene name='Sandbox2442/N-ter_domain/4'>an αβαβα five-layered structure</scene>. The <scene name='Sandbox2442/C-ter_domain/3'>C-ter domain</scene> (residues 440-550) forms a small
<scene name='Sandbox2442/C-ter_domain/4'>α+ β domain</scene>.

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='Sandbox2442/N-ter_c-ter/1'>C-domain relative to the N-domain</scene><ref name="ane">PMID:17513367</ref>

===Sequence similarities===
The firefly luciferase shares homologuous sequences and mechanisms with the peptide synthetases and acyl-CoA ligases, with a very few residues always conserved.
The firefly luciferase belongs to the super-family of acyl-adenylate-forming and thioester-forming enzymes.

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 O2. So differents groups of residues are part of the the ligand binding.
Those residues can be placed in the molecule by comparing the sequences of different enzymes of the same family.
The ATP binds to a <scene name='Sandbox2442/Atp_binding/1'>206 G-x-x-x-x-x-G-K-[STG]196</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 he 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:

* Thr 346 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.

* Asp 422 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.

* The Ser420 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/1'>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.

==Applications of the luciferase==
Luciferase can be used to measure ATP <ref>Hawronskyj J.-M, Measurement of ATP using firefly luminescence. European food and drink review. 1997, SUMMER, pp. 61-63 ISSN [http://cat.inist.fr/?aModele=afficheN&cpsidt=2717464 0955-4416]</ref>
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.

==Chemical reaction==

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

* luciferin + ATP → luciferyl adenylate + PPi

* luciferyl adenylate + O2 → oxyluciferin + AMP + light

The first half-reaction is an adenylation, the second one is an oxydative decarboxylation.

The production of light is achieved by the conversion of chemical energy into an emission of photons, resulting from the passage of the oxyluciferin's excitation state to a ground state.

==Spectral difference with mutated luciferases==

The colour changes from the classical yellow-green colour to red with the substitution of a single amino acid, Ser 286 to Asn, in the S286N mutant. The active site (and the residue Ile 288) 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>

==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 [http://en.wikipedia.org/wiki/Firefly fireflies] use bioluminescence to locate other indivuduals 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.

==References==
<references />

Japanese firefly Luciferase complexed with Oxyluciferin & AMP

2009-11-18T16:06:07Z

Loïc Gazquez: /* The structure */

[[Image:2d1r.png|left|200px]]


{{STRUCTURE_2d1r| PDB=2d1r | SCENE= }}

=Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP=

==Introduction==

Luciferase is a class of enzymes producing light through the process of bioluminescence. This luciferase was extracted from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. In the case of fireflies, it 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.

==The structure==
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.

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. <scene name='Sandbox2442/N-ter_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
<scene name='Sandbox2442/N-ter_domain/4'>an αβαβα five-layered structure</scene>. The <scene name='Sandbox2442/C-ter_domain/3'>C-ter domain</scene> (residues 440-550) forms a small
<scene name='Sandbox2442/C-ter_domain/4'>α+ β domain</scene>.

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='Sandbox2442/N-ter_c-ter/1'>C-domain relative to the N-domain</scene><ref name="ane">PMID:17513367</ref>

===Sequence similarities===
The firefly luciferase shares homologuous sequences and mechanisms with the peptide synthetases and acyl-CoA ligases, with a very few residues always conserved.
The firefly luciferase belongs to the super-family of acyl-adenylate-forming and thioester-forming enzymes.

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 O2. So differents groups of residues are part of the the ligand binding.
Those residues can be placed in the molecule by comparing the sequences of different enzymes of the same family.
The ATP binds to a <scene name='Sandbox2442/Atp_binding/1'>206 G-x-x-x-x-x-G-K-[STG]196</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 he 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:

* Thr 346 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.

* Asp 422 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.

* The Ser420 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/1'>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.

==Applications of the luciferase==
Luciferase can be used to measure ATP <ref>Hawronskyj J.-M, Measurement of ATP using firefly luminescence. European food and drink review. 1997, SUMMER, pp. 61-63 ISSN [http://cat.inist.fr/?aModele=afficheN&cpsidt=2717464 0955-4416]</ref>
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.

==Chemical reaction==

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

* luciferin + ATP → luciferyl adenylate + PPi

* luciferyl adenylate + O2 → oxyluciferin + AMP + light

The first half-reaction is an adenylation, the second one is an oxydative decarboxylation.

The production of light is achieved by the conversion of chemical energy into an emission of photons, resulting from the passage of the oxyluciferin's excitation state to a ground state.

==Spectral difference with mutated luciferases==

The colour changes from the classical yellow-green colour to red with the substitution of a single amino acid, Ser 286 to Asn, in the S286N mutant. The active site (and the residue Ile 288) 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>

==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 [http://en.wikipedia.org/wiki/Firefly fireflies] use bioluminescence to locate other indivuduals 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.

==References==
<references />

Japanese firefly Luciferase complexed with Oxyluciferin & AMP

2009-11-18T15:58:08Z

Loïc Gazquez: /* The structure */

[[Image:2d1r.png|left|200px]]


{{STRUCTURE_2d1r| PDB=2d1r | SCENE= }}

=Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP=

==Introduction==

Luciferase is a class of enzymes producing light through the process of bioluminescence. This luciferase was extracted from [http://en.wikipedia.org/wiki/Luciola_cruciata Luciola cruciata]. In the case of fireflies, it 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.

==The structure==
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.

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. <scene name='Sandbox2442/N-ter_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
<scene name='Sandbox2442/N-ter_domain/3'>an αβαβα five-layered structure</scene>. The <scene name='Sandbox2442/C-ter_domain/3'>C-ter domain</scene> (residues 440-550) forms a small
<scene name='Sandbox2442/C-ter_domain/4'>α+ β domain</scene>.

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='Sandbox2442/N-ter_c-ter/1'>C-domain relative to the N-domain</scene><ref name="ane">PMID:17513367</ref>

===Sequence similarities===
The firefly luciferase shares homologuous sequences and mechanisms with the peptide synthetases and acyl-CoA ligases, with a very few residues always conserved.
The firefly luciferase belongs to the super-family of acyl-adenylate-forming and thioester-forming enzymes.

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 O2. So differents groups of residues are part of the the ligand binding.
Those residues can be placed in the molecule by comparing the sequences of different enzymes of the same family.
The ATP binds to a <scene name='Sandbox2442/Atp_binding/1'>206 G-x-x-x-x-x-G-K-[STG]196</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 he 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:

* Thr 346 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.

* Asp 422 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.

* The Ser420 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/1'>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.

==Applications of the luciferase==
Luciferase can be used to measure ATP <ref>Hawronskyj J.-M, Measurement of ATP using firefly luminescence. European food and drink review. 1997, SUMMER, pp. 61-63 ISSN [http://cat.inist.fr/?aModele=afficheN&cpsidt=2717464 0955-4416]</ref>
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.

==Chemical reaction==

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

* luciferin + ATP → luciferyl adenylate + PPi

* luciferyl adenylate + O2 → oxyluciferin + AMP + light

The first half-reaction is an adenylation, the second one is an oxydative decarboxylation.

The production of light is achieved by the conversion of chemical energy into an emission of photons, resulting from the passage of the oxyluciferin's excitation state to a ground state.

==Spectral difference with mutated luciferases==

The colour changes from the classical yellow-green colour to red with the substitution of a single amino acid, Ser 286 to Asn, in the S286N mutant. The active site (and the residue Ile 288) 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>

==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 [http://en.wikipedia.org/wiki/Firefly fireflies] use bioluminescence to locate other indivuduals 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.

==References==
<references />