All the initial portions of this page were created by [[User:James Jones|James Jones]] and were moved because it deserved its own separate page distinct from the associated PDB entry.
All the initial portions of this page were created by [[User:James Jones|James Jones]] and were moved because it deserved its own separate page distinct from the associated PDB entry.
</StructureSection>
==3D structures of luciferase==
==3D structures of luciferase==
Latest revision as of 12:42, 8 July 2018
Luciferase domain from a Dinoflagellate. Selenomethionines shown as space-filling objects 1vpr
Lingulodinium polyedrum, a marine dinoflagellate often responsible for red tide, possesses 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.
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 [1]
Structure
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[1]. 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[1].
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.
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[2]. 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.
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 courtesy of L. Wayne Schultz.
References
↑ 1.01.11.2Schultz 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
↑Okamoto OK, Liu L, Robertson DL, Hastings JW. Members of a dinoflagellate luciferase gene family differ in synonymous substitution rates. Biochemistry. 2001 Dec 25;40(51):15862-8. PMID:11747464
Content Donors
All the initial portions of this page were created by James Jones and were moved because it deserved its own separate page distinct from the associated PDB entry.
