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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' />




== Introduction ==
== 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.
''Lingulodinium polyedrum'', a marine dinoflagellate often responsible for red tide, posesses a unique luciferase enyzme. When mechanically stimulated, the organism uses this enzyme to produce a blue light, likely for use in quorum sensing. Other luciferase enzymes typically produce green-yellow to red light. Also, while all luciferase enzymes produce light through oxidation of luciferin, the biochemical mechanism by which this is achieved is different, so the lack of similarity to firefly and bacterial luciferases is expected.  
In ''L. polyedrum'', the luciferase enzyme is a single polypeptide chain folded into 3 similiar domains. Only domain 3 (the structure presented here) appears to participate in the luciferin reaction.  
 
 


== Structure ==
== Structure ==
Composed of residues 868-1218, domain 3 (D3) also consists of a 20aa c domain, but said region was unable to be solved due to high disorder in the region. Composed of 7 α-helices and 16 β-strands, D3 is further organized into subdomains. The main portion of the enzyme appears to be a β-barrel structure composed of 10 antiparrallel strands connected via a Gly rich sequence to a 3 helix bundle. This bundle is stabilized by a hydrophobic core region as well as a multitude of H-bonding patterns. The β-barrel structure actually has some homology with the human muscle fatty acid binding protein (m-FABP, pdb= 1HMT). This, and other related proteins, form a "β-clam" subdomain structure for binding of hydrophobic molecules. However, other known β-clam structures do not possess enzymatic activity.  
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]


== Luciferase Reaction ==
[http://www.pdb.org/pdb/explore/explore.do?structureId=2D1S Protein Data Bank file on 2D1S]


Typically, luciferases produce light through a high energy complex with a luciferin cofactor, and Mg-ATP. The structure of luciferin is different from organism to organism, and in ''L. polyedrum'', is a chlorophyll-derived tetrapyrrole. Below is the dinoflagellate luciferase reaction, showing the oxidation site.
[http://www.ncbi.nlm.nih.gov/protein/CAA59282.1 NCBI protein entry on ''Photinus pyralis'' luciferase, the american firefly]
[[Image:Luciferase_reaction.jpg]]


''Image courtesy of L. Wayne Schultz.''
== References ==
<references />

Latest revision as of 02:14, 22 August 2010

PDB ID 2d1s

Drag the structure with the mouse to rotate
2d1s, resolution 1.30Å ()
Ligands: ,
Non-Standard Residues:
Activity: Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing), with EC number 1.13.12.7
Related: 2d1r, 2d1t
Resources: FirstGlance, OCA, PDBsum, RCSB, TOPSAN
Coordinates: save as pdb, mmCIF, xml




IntroductionIntroduction

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". [1] 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.

StructureStructure

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.[2]. 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. [2].

Figure 1: PYMOL image of 2D1S highlighting active site and Ile288, putatively identified in hydrophobic control of bioluminescent colour.

Related LinksRelated Links

Pymol molecular viewer

Protein Data Bank file on 2D1S

NCBI protein entry on Photinus pyralis luciferase, the american firefly

ReferencesReferences

  1. ↑ Suzuki H, Sato Y, Fujiyama S, Ohba N. Biochemical systematics of Japanese fireflies of the subfamily Luciolinae and their flash communication systems. Biochem Genet. 1996 Jun;34(5-6):191-200. PMID:8813052
  2. ↑ 2.0 2.1 Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H. Structural basis for the spectral difference in luciferase bioluminescence. Nature. 2006 Mar 16;440(7082):372-6. PMID:16541080 doi:10.1038/nature04542

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