Sandbox 167: Difference between revisions

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Andrea Gorrell, James Jones

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-'''Lingulodinium polyedrum dinoflagellate luciferase'''
+{{STRUCTURE_2d1s|  PDB=2d1s  |  SCENE=  }}
-<applet load='1vpr' size='300' frame='true' align='right' caption='Insert caption here' />
-Lingulodinium polyedrum, a marine dinoflagellate often responsible for red tide, posesses a unique-domain luciferase enyzme. When mechanically stimulated, the organism uses this enzyme to produce a blue light, likely for use in quorum sensing.
 == Introduction ==
+Bioluminescence is 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.
-In ''L. polyedrum'', the luciferase enzyme is a single polypeptide chain folded into 3 similiar domains. Each domain participates in its own reaction with luciferin, allowing for simultaneous luciferase reactions to take place on the same protein.
+== Structure ==
+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>.
+The DLSA occupied the active site of the luciferase, which is composed of an α-helix (residues 248-260) and four short β-sheets (residues 286-289, 313-316, 339-342 and 351-353. Ile288 has been implicated as an important residue in determining the hydrophobicity of the active site environment, and through orientation of the product oxyluciferin, the bioluminescent colour. <ref name="structure" />.
+[[Image:2d1s active site with ILE288.jpg | thumb |none | upright=3.0 | Figure 1: PYMOL image of 2D1S highlighting active site and Ile288, putatively identified in hydrophobic control of bioluminescent colour.]]
+== Related Links ==
+[http://www.pymol.org/ Pymol molecular viewer]
+[http://www.pdb.org/pdb/explore/explore.do?structureId=2D1S Protein Data Bank file on 2D1S]
+[http://www.ncbi.nlm.nih.gov/protein/CAA59282.1 NCBI protein entry on ''Photinus pyralis'' luciferase, the american firefly]
-== Luciferase Reaction ==
+== References ==
+<references />
-The active site