User:Mitchell Long/Sandbox 1: Difference between revisions
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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. 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 strans of the TIM-barrel structure. 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>'''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 strans of the TIM-barrel structure. 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. | ||
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<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> | ||
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(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> | ||
