Sandbox 167

2010-08-18T23:33:43Z

James Jones: /* Structure */

File:2d1s active site with ILE288.jpg

2010-08-18T23:32:39Z

2010-03-24T17:53:03Z

James Jones:

{{STRUCTURE_1vpr| PDB=1vpr | SCENE= }}
<scene name='colorSTRUCTURE'>structure</scene>

== Introduction ==

''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. Interestingly, all three domains appear to be distinct luciferase centres with their own catalytic activities.

== 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.

Cropped Pymol image of 1vpr highlighting the β-barrel structure and tri-helix. The four histidine residues implied in pH-dependant activity regulation are highlighted in pink.

[[Image:Structure_trihelix_barrel.jpg ]]

Note the position of the tri-helix in front of the β-barrel opening, blocking substrate entry. Under pH 8, the protonation states of the four histidines are thought to drive a conformational change that opens and expands the β-barrel.

== Luciferase Reaction ==

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 open-tetrapyrrole. Below is the dinoflagellate luciferase reaction, showing the oxidation site.
[[Image:Luciferase_reaction.jpg]]

''Image courtesy of L. Wayne Schultz.''

== References ==
<ref>PMID:15665092</ref>

Sandbox 167

2010-03-24T17:49:56Z

James Jones:

File:Structure trihelix barrel.jpg

2010-03-24T16:24:56Z

James Jones: uploaded a new version of "Image:Structure trihelix barrel.jpg": Cropped PyMol image of 1vpr highlighting the tri-helix and beta-barrel structure. Note that residues implied in pH-depentant activity regulation are coloured pink.

== Summary ==
Cropped PyMol image of 1vpr highlighting the tri-helix and beta-barrel structure. Note that residues implied in pH-depentant activity regulation are coloured pink.
== Licensing ==
{{self|cc-by-3.0}}

Sandbox 167

2010-03-22T20:06:30Z

James Jones:

'''Lingulodinium polyedrum dinoflagellate luciferase'''
{{STRUCTURE_1vpr| PDB=1vpr | SCENE= }}

== Introduction ==

''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. Interestingly, all three domains appear to be distinct luciferase centres with their own catalytic activities.

== 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.

== Luciferase Reaction ==

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 open-tetrapyrrole. Below is the dinoflagellate luciferase reaction, showing the oxidation site.
[[Image:Luciferase_reaction.jpg]]

''Image courtesy of L. Wayne Schultz.''

== References ==