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Sandbox 167

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{{STRUCTURE_1vpr| PDB=1vpr | SCENE= }}
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{{STRUCTURE_2d1s| PDB=2d1s | SCENE= }}
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== Introduction ==
== Introduction ==
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''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 varies. This means that while the result is the same, there is low similarity to bacterial or firefly luciferases.
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Japanese firefly. <ref name="main">PMID:15665092</ref>
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In ''L. polyedrum'', the luciferase enzyme is a single polypeptide chain folded into 3 similar domains. Interestingly, all three domains appear to be distinct luciferase centres with their own catalytic activities <ref name="main">PMID:15665092</ref>
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== Structure ==
== Structure ==
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Composed of residues 868-1218, domain 3 (D3) also consists of a 20aa C-terminal unresolved domain. Containing 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 anti-parallel 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<ref name="main" />. The β-barrel structure actually has some homology with the human muscle fatty acid binding protein (m-FABP, pdb= 1HMT). Both are part of a "β-clam" subdomain family, responsible for binding of hydrophobic molecules. However, other known β-clam structures do not possess enzymatic activity<ref name="main" />.
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Structure of japanese firefly luciferase.<ref name="main" />. The β-barrel structure actually has some homology with the human muscle fatty acid binding protein (m-FABP, pdb= 1HMT).
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[[Image:IMAGENAMEHERE.jpg | thumb |none | upright=3.0 | Figure 1: Caption for figure 1]]
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Notes about the image
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[[Image:Structure_trihelix_barrel.jpg | thumb |none | upright=3.0 | Figure 1: 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.]]
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Second image
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Notes about the image
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Note the position of the tri-helix in front of the β-barrel opening, blocking substrate entry. Under a pH of 8, the protonation states of the four histidines are thought to drive a conformational change that opens and expands the β-barrel. Interestingly, the four histidines(H899, H909, H924 and H930) are conserved in another dinoflagellate, ''Pyrocystis lunula''<ref name="papertwo">PMID:11747464</ref>. This seems to suggest a pH-dependant luciferase contol mechanism similiar to the proposed mechanism in ''L. polyedrum''. While related at the primary structure level, the structure of ''P. lunula'' luciferase has yet to be solved, so further structural similarities cannot be easily determined.
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== Luciferase Reaction ==
== Luciferase Reaction ==
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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.
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Typically, luciferases produce light through a high energy complex with a luciferin cofactor, and Mg-ATP.
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[[Image:Luciferase_reaction.jpg]]
 
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''Image courtesy of L. Wayne Schultz.''
 

Revision as of 01:07, 20 July 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




Contents

Introduction

Japanese firefly. [1]

Structure

Structure of japanese firefly luciferase.[1]. The β-barrel structure actually has some homology with the human muscle fatty acid binding protein (m-FABP, pdb= 1HMT).

Image:IMAGENAMEHERE.jpg
Figure 1: Caption for figure 1
Notes about the image

Second image

Notes about the image

Luciferase Reaction

Typically, luciferases produce light through a high energy complex with a luciferin cofactor, and Mg-ATP.




Related Links

Pymol molecular viewer

Protein Data Bank file on 1VPR

NCBI protein entry on P. lunula luciferase

References

  1. ↑ 1.0 1.1 Schultz LW, Liu L, Cegielski M, Hastings JW. Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1378-83. Epub 2005 Jan 21. PMID:15665092
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