User:Mitchell Long/Sandbox 1: Difference between revisions
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==Mechanism== | ==Mechanism== | ||
Luciferase found in''''V. Harveyi'''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons | Luciferase found in''''V. Harveyi'''' binds noncovalently to a reduced flavin mononucleotide cofactor, an aliphatic aldehyde and oxygen to yield oxidized flavin mononucleotide, water, and carboxylic acid. The reaction occurs in two steps forming a hydroxyflavin intermediate and ultimately results in the oxidation of the aldehyde and emission of photons<ref Campbell, Z.T.>PMID: 19435287</ref>. | ||
<p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p> | <p>FMNH<sub>2</sub>+O<sub>2</sub>+RCHO→FMN+RCOOH+H<sub>2</sub>O+hv(490nm)</p> | ||
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<p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement. In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β | <p>'''Structure homology'''-There is a great deal of sequence homology and structural coservation between the α and β subunits. When superimposed over the barrels of the alpha and beta subunits with a deviation of 0.62Å for 42 equivalent α carbons. The region of the beta subunit that contains the 29 residue deletion with respect to the alpha subunit differs notably in arrangement<ref name=Fisher, A.J.>PMID: 7756289</ref> . In the alpha subunit, the α7a helix is straight and extends toward the beta subunit. The region involved with dimerization, helices α and β are exceptionally similar in superposition. | ||
</p> | </p> | ||
<p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ | <p>'''Active Site and Alpha Subunit'''-the <scene name='User:Mitchell_Long/Sandbox_1/Yellow_sheets/1'>flavin binding pocket</scene> of bacterial luciferase is a large open cavity that is accessible to solvent via an opening located at the C-terminal ends of the ǰ strands of the TIM-barrel structure<ref Campbell, Z.T.>PMID: 19435287</ref>. During the first step of the oxidation reaction, FMNH<sub>2</sub> binds to the flavin binding pocket and the enzyme undergoes a conformational change that blocks water in the surrounding environment from accessing both the excited peroxydihydroflavin intermediate. Next, O<sub>2</sub> and a long chain aldehyde bind to the FMNH<sub>2</sub> luciferase complex and a two step oxidatino reaction occurs. | ||
.</p> | .</p> | ||
<scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene> | <scene name='User:Mitchell_Long/Sandbox_1/Hetero_translucent/1'>Heterodimer</scene> | ||
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<p><scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene></p> | <p><scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene></p> | ||
<p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic &# | <p>'''The β subunit'''-The beta subunit is characterized as a necessary but non-catalytic subunit that stabilizes the catalytic α subunit that is responsible for the oxidation reaction. The beta and alpha subunits are connected by a single interaction between the <scene name='User:Mitchell_Long/Sandbox_1/Phe272_tyr151_interface/1'>Phe 272 Tyr 151 interface</scene> | ||
</p> | </p> | ||
<p>'''Mobile Loop'''- | <p>'''Mobile Loop'''- Residues 272-288 on the α are known as the mobile loop. This portion of the alpha subunit contains a single residue that forms a salt bridge with the beta subunit and stabilizes the active site<ref Campbell, Z.T.>PMID: 19435287</ref>. | ||
(β/α)<SUB>8</SUB> Barrel- The tertiary structure of the α and β subunits is very similar. both subunits fold into a single-domain eight-stranded β/α barrel motif. the two subunits assemble around a parallel four-helix bundle centered on a pseudo 2-fold axis that relates the alpha and beta subunits. | </p> | ||
<p> | |||
(β/α)<SUB>8</SUB> TIM Barrel- The tertiary structure of the α and β subunits is very similar. While both the alpha and beta subunits are similar, the alpha subunit contains an extra 29 residues that the beta lacks. Both subunits fold into a single-domain eight-stranded β/α barrel motif. the two subunits assemble around a parallel four-helix bundle centered on a pseudo 2-fold axis that relates the alpha and beta subunits<ref Campbell, Z.T.>PMID: 19435287</ref>. | |||
.</p> | .</p> | ||
</StructureSection> | </StructureSection> | ||
