Sandbox Reserved 1644: Difference between revisions

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<p align="justify">The '''active site''' represent by 2x36 is composed of''' six [https://en.wikipedia.org/wiki/Protomer protomers]''' in the asymmetric unite. One protomer counts nine [https://en.wikipedia.org/wiki/Beta_sheet b-strands] and seven [https://en.wikipedia.org/wiki/Alpha_helix a-helices]. An analysis of the complex’ structure suggested that '''two pair of protomers''' form A:B and C:D dimers and that the '''two''' remaining ones remain '''uncoupled'''. The dimer interface A:B/C:D is mostly linked by one another through '''hydrophilic interactions''', where the a1-helix is packed against the b3-strand and the loop between b7 and b8 makes inter-subunit contacts with b2<ref>PMID: 20222013</ref>.

As all LonA proteins, ''h''Lon catalytic activity relies on a '''Ser-Lys dyad'''. Ser855 on a2 conducts the catalytic cleavage with the assistance of Lys898 on a3 through their [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen-bonding]. The lysine works as a general [https://en.wikipedia.org/wiki/Base_(chemistry) base] along with Thr880 which, in their deprotonated form, abstract the proton from the [https://en.wikipedia.org/wiki/Nucleophile nucleophilic] serine. Those three residues constitute the <scene name='86/868177/Hlonp_catalytic_core/1'>catalytic core</scene>. A characteristic of ''h''LonP is that the [https://en.wikipedia.org/wiki/310_helix 3(10)] helix at the N-terminal end of a2 is able to bring an '''additional residue into the active site''', Asp852. This most likely enables Lys898 [https://en.wikipedia.org/wiki/Acid_dissociation_constant pKa] lowering by creating a [https://en.wikipedia.org/wiki/Hydrophobe hydrophobic] environment, and thus, prevents the dyad to cut off protein substrates. This catalytic '''inactive form''' is also supported by the Asp852 and Trp770 residues that contribute to the <scene name='86/868177/Hlonp_closed_catalitic_core/1'>catalytic site obstruction</scene>. Asp852 removal from the active site through conformational changes enables ''h''Lon to reach an open state that can hydrolyze protein substrate through ATP consumption<ref>PMID: 20222013</ref>.</p>

<br> The figure below shows a 3D simulation of the 2x36 protein, in which the catalytic core (in green) and the catalytic site obstruction (in ~~grey~~) are highlighted and can be more easily observed.

<br> The figure below shows a 3D simulation of the 2x36 protein, in which the catalytic core (in green) and the catalytic site obstruction (in gray) are highlighted and can be more easily observed.

[[Image:2x36as.png]]

Sandbox Reserved 1644: Difference between revisions

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@@ Line 80: / Line 80: @@
 <p align="justify">The '''active site''' represent by 2x36 is composed of''' six [https://en.wikipedia.org/wiki/Protomer protomers]''' in the asymmetric unite. One protomer counts nine [https://en.wikipedia.org/wiki/Beta_sheet b-strands] and seven [https://en.wikipedia.org/wiki/Alpha_helix a-helices]. An analysis of the complex’ structure suggested that '''two pair of protomers''' form A:B and C:D dimers and that the '''two''' remaining ones remain '''uncoupled'''. The dimer interface A:B/C:D is mostly linked by one another through '''hydrophilic interactions''', where the a1-helix is packed against the b3-strand and the loop between b7 and b8 makes inter-subunit contacts with b2<ref>PMID: 20222013</ref>.
 As all LonA proteins, ''h''Lon catalytic activity relies on a '''Ser-Lys dyad'''. Ser855 on a2 conducts the catalytic cleavage with the assistance of Lys898 on a3 through their [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen-bonding]. The lysine works as a general [https://en.wikipedia.org/wiki/Base_(chemistry) base] along with Thr880 which, in their deprotonated form, abstract the proton from the [https://en.wikipedia.org/wiki/Nucleophile nucleophilic] serine. Those three residues constitute the <scene name='86/868177/Hlonp_catalytic_core/1'>catalytic core</scene>. A characteristic of ''h''LonP is that the [https://en.wikipedia.org/wiki/310_helix 3(10)] helix at the N-terminal end of a2 is able to bring an '''additional residue into the active site''', Asp852. This most likely enables Lys898 [https://en.wikipedia.org/wiki/Acid_dissociation_constant pKa] lowering by creating a [https://en.wikipedia.org/wiki/Hydrophobe hydrophobic] environment, and thus, prevents the dyad to cut off protein substrates. This catalytic '''inactive form''' is also supported by the Asp852 and Trp770 residues that contribute to the <scene name='86/868177/Hlonp_closed_catalitic_core/1'>catalytic site obstruction</scene>. Asp852 removal from the active site through conformational changes enables ''h''Lon to reach an open state that can hydrolyze protein substrate through ATP consumption<ref>PMID: 20222013</ref>.</p>
-<br> The figure below shows a 3D simulation of the 2x36 protein, in which the catalytic core (in green) and the catalytic site obstruction (in grey) are highlighted and can be more easily observed.
+<br> The figure below shows a 3D simulation of the 2x36 protein, in which the catalytic core (in green) and the catalytic site obstruction (in gray) are highlighted and can be more easily observed.
 [[Image:2x36as.png]]