NodS: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Marcin Jozef Suskiewicz, David Canner, Michal Harel, Alexander Berchansky

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 During the NodS-catalyzed reaction, the chitooligosaccharide substrate is methylated while the methyl donor, S-adenosyl-L-methionine, is transformed into S-adenosyl-L-homocysteine. The latter product is, however, chemically still highly similar to S-adenosyl-L-methionine and hence
 <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/3/1'>the structure of NodS bound to S-adenosyl-L-homocysteine</scene> gives reliable representation of the binding mode of both S-adenosyl-L-homocysteine and, by inference, S-adenosyl-L-methionine to the enzyme. Notice the position of the
-<scene name='NodS/3/3'>helix A</scene> (the most N-terminal), which was not visible in the apo form, but got structured upon ligand binding; this helix, unlike others, is positioned on top of the β-sheet structure, not on its side, and is <scene name='NodS/3/2'>in close proximity to the ligand</scene>. There are many other small changes in the structure of ligand-bound NodS when compared to the apo form, mainly around the binding cavity, but the deviations do not exceed 0.9 Å. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/3/2'>S-adenosyl-L-homocysteine</scene>-binding cavity is predominately hydrophobic, but numerous polar interactions are likely to play a role in positioning the ligand in its specific orientation. There are <scene name='NodS/2/1'>11 polar interactions</scene> between NodS residues and S-adenosyl-L-methionine ligand and around 5-7 additional ones between the water molecules present in the binding pocket and the ligand. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/4'>amino group of the homocysteine amino acid moiety is anchored</scene> by the main-chain carbonyl groups of Gly 52 and Ala 114 from loop β1–αC and strand β4, respectively. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/5'>carboxy group of the same moiety interacts</scene> with the side chains of the basic amino acid residues Arg 31 and His 32 in helix αB. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/7'>hydroxyl groups of the ribose fragment of S-adenosyl-L-homocysteine form</scene> a pair of forked hydrogen bonds with both oxygen atoms of the carboxylic group of Asp 73 and a single hydrogen bond with main-chain nitrogen of Ala 54, Asp 73 being located at the tip of the β2 strand and Ala 54 in loop β1–αC. Finally, <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/8'>the adenine ring of the ligand is interacting</scene> with the main-chain nitrogen of Ile 99 and by the side chain of Asp 98, both from the β3–β4 loop. This adenine ring is also capable of making CH-π interactions with aliphatic side chains of valines 74 and 116. <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/9'>An additional interaction</scene> can potentially be formed between the sulfonium group of the ligand and the π system of Trp 20 when the methyl donor, S-adenosyl-L-methionine is bound instead of the homocysteine derivative. This interaction is likely to contribute to the larger affinity of NodS towards the methyl donor (a substrate) comparing to the homocysteine derivative (a products). The overall positioning of the methyl donor inside the protein is such that it is <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/4/1'>guarded from the environment</scene>, but the fragment of it where the methyl group of S-adenosyl-L-methionine is located <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/4/2'>is exposed</scene> to the putative substrate-binding canyon. The canyon is roughly 22 Å long, 10.5 Å wide and 10.5 Å deep. It is located near the N-terminal end of helix αB and the C-terminal end of strand β4. No structure of NodS with the substrate bound is available, but computational docking suggests that this canyon is indeed an energetically favourable binding site, mainly due to a number of possible polar interactions.<ref>PMID: 20970431</ref>
+<scene name='NodS/3/3'>helix A</scene> (the most N-terminal), which was not visible in the apo form, but got structured upon ligand binding; this helix, unlike others, is positioned on top of the β-sheet structure, not on its side, and is <scene name='NodS/3/2'>in close proximity to the ligand</scene>. There are many other small changes in the structure of ligand-bound NodS when compared to the apo form, mainly around the binding cavity, but the deviations do not exceed 0.9 Å. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/3/2'>S-adenosyl-L-homocysteine</scene>-binding cavity is predominately hydrophobic, but numerous polar interactions are likely to play a role in positioning the ligand in its specific orientation. There are
+<scene name='NodS/Domek/2'>11 polar interactions</scene> between NodS residues and S-adenosyl-L-methionine ligand and around 5-7 additional ones between the water molecules present in the binding pocket and the ligand. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/4'>amino group of the homocysteine amino acid moiety is anchored</scene> by the main-chain carbonyl groups of Gly 52 and Ala 114 from loop β1–αC and strand β4, respectively. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/5'>carboxy group of the same moiety interacts</scene> with the side chains of the basic amino acid residues Arg 31 and His 32 in helix αB. The <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/7'>hydroxyl groups of the ribose fragment of S-adenosyl-L-homocysteine form</scene> a pair of forked hydrogen bonds with both oxygen atoms of the carboxylic group of Asp 73 and a single hydrogen bond with main-chain nitrogen of Ala 54, Asp 73 being located at the tip of the β2 strand and Ala 54 in loop β1–αC. Finally, <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/8'>the adenine ring of the ligand is interacting</scene> with the main-chain nitrogen of Ile 99 and by the side chain of Asp 98, both from the β3–β4 loop. This adenine ring is also capable of making CH-π interactions with aliphatic side chains of valines 74 and 116. <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/2/9'>An additional interaction</scene> can potentially be formed between the sulfonium group of the ligand and the π system of Trp 20 when the methyl donor, S-adenosyl-L-methionine is bound instead of the homocysteine derivative. This interaction is likely to contribute to the larger affinity of NodS towards the methyl donor (a substrate) comparing to the homocysteine derivative (a products). The overall positioning of the methyl donor inside the protein is such that it is <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/4/1'>guarded from the environment</scene>, but the fragment of it where the methyl group of S-adenosyl-L-methionine is located <scene name='User:Marcin_Jozef_Suskiewicz/Sandbox_MarcinSuskiewicz/4/2'>is exposed</scene> to the putative substrate-binding canyon. The canyon is roughly 22 Å long, 10.5 Å wide and 10.5 Å deep. It is located near the N-terminal end of helix αB and the C-terminal end of strand β4. No structure of NodS with the substrate bound is available, but computational docking suggests that this canyon is indeed an energetically favourable binding site, mainly due to a number of possible polar interactions.<ref>PMID: 20970431</ref>
 </StructureSection>