User:Mitchell Long/Sandbox 1: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 6: | Line 6: | ||
==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> | ||
| Line 21: | Line 21: | ||
<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>'''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> | ||
| Line 28: | Line 28: | ||
<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> | ||
