Sandbox Reserved 951
From Proteopedia
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===Interactions with ligands=== | ===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. They follow a cleft caused by of the β sheet against the <scene name='60/604470/Beta_barrel/2'>β barrel</scene>. | + | 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. They follow a <scene name='60/604470/Cleft/1'>cleft</scene> caused by of the β sheet against the <scene name='60/604470/Beta_barrel/2'>β barrel</scene>. |
However, this cleft 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. | However, this cleft 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. | ||
=====Interaction with ATP===== | =====Interaction with ATP===== | ||
Revision as of 18:44, 8 January 2015
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Contents |
Biological role
The different reactions
Light emission
The most known reaction of luciferase is the light emission. In this reaction, luciferase firstly synthetized luciferin-AMP from luciferin and ATP, using a Mg2+ ion to offset the negative charges of the phosphate groups. Then, luciferase turns the luciferin-AMP into oxyluciferin in an excited state thanks to a dioxygen. This step releases AMP and CO2. The excited oxyluciferin relaxes and looses a photon so light is emitted. The wavelength of the light can vary with the pH : at the physiological pH, the emitted light is green and at a lower pH, the color is red.
Fatty-acyl-CoA synthesis
This reaction uses similar reaction but instead of taking luciferin as ligand, it takes fatty acids. Using ATP-Mg2+, it firstly forms fatty-acyl-AMP. And then, CoA-SH attacks the carboxylic group of fatty-acyl-AMP and so forms fatty-acyl-CoA.
Luciferin & Coenzyme A
It has been found that the reaction between luciferin and CoA is possible, forming in a first step luciferin-AMP and then luciferin-CoA. This reaction leads to an interesting biological phenomenon : when this reaction occurs in parallel of light emission reaction, we don't have a flash of light but a continuous light emission. This is because luciferin-AMP is a competitive inhibitor of the reaction whereas the luciferin-CoA is not. So the inhibition is deleted and the reaction continue to occur.
Global Structure
Function highlighted with structure
The most known reaction of luciferase is the light emission where luciferase uses luciferin, ATP and O2 as substrates. The color of emitted light varies according to the pH, which can be explained by the luciferase structure. But there are some other reactions which can uses fatty acids and coenzyme A. So the active site of the luciferase can theorically bind all these compounds.
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. They follow a caused by of the β sheet against the . However, this cleft 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.
Interaction with ATP
We find a signal motif in luciferase which is 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 : [YFW]-[GASW]-x-[TSA]-E which takes a particular conformation because of hydrogen bonds between residues and maintain the adenosin ring of ATP.
Interaction with luciferin
Luciferase holds the luciferin with the specific residues arginin 218, phenylalanin 247, serin 347 and adenin 348, 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.
Interaction with fatty acids
Fatty acids are highly similar to luciferin. Therefore, luciferase can use the luciferin binding site to bind fatty acids. That is why they can be used as substrates by luciferase and then, very high similar reaction as for luciferin occurs.
Color modulation
When the pH is low, the color of light changes. This is probably due to the hydrogen bonds network between substrates, residues of the cleft and water. Indeed, this network triggers to an external electrostatic potential which stabilizes a charge created during the reaction of light emission. The lower pH leads to a weakening of the network, so the energy which can be emitted decreases and the wavelength of photon increases and becomes more red.
Evolution
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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