Sandbox Reserved 1107: Difference between revisions

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== Asymmetric and biological unit ==

The basal 3D scene shown on this page corresponds to the asymmetric unit, which contains 4 biological units of MraYAA (colors), which each of them is fused with the NB7 nanobody (teal). Mashalidis EH, Kaeser Bet al. , who solved this 3D structure, were screening antibodies. They determine that the presence of NB7 does not affect MraYAA enzymatic activity or inhibition by carbacaprazamycin <ref name="seven"/>.

The basal 3D scene shown on this page corresponds to the asymmetric unit, which contains 4 <scene name='82/829360/4_biological_units/2'>biological units</scene> of MraYAA (colors), which each of them is fused with the NB7 nanobody (teal). Mashalidis EH, Kaeser Bet al. , who solved this 3D structure, were screening antibodies. They determine that the presence of NB7 does not affect MraYAA enzymatic activity or inhibition by carbacaprazamycin <ref name="seven"/>.

== MraY-Carbacaprazamycin structure ==

In bacteria, MraYAA is in the form of a dimer, which actually what researchers found in the first 3D structure of MraYAA <ref name="three"/>. Its N and the C termini are located on the periplasmic side. This protein is made of four extracellular loops, five cytoplasmic loops (named A,B, C, D and E) and ten transmembrane helices named TM1 to TM10. Though, TM9 is cleaved by a glycin residue into two helical segments named TM9a and TM9b. Furthermore, there is an additional helix between TM9b and TM10, which is only 11 residues long and is called TM9c. TM9c contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H324,325 and 326) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. They intereact with carbacaprazamycin, and also with other inhibitors such as [http://proteopedia.org/wiki/index.php/5ckr muraymycin D2 (MD2) ]. This small loop binds two Ni2+ ions, one on the two first histidines and the other one on the last one. Another part of this site is the residues corresponding to <scene name='42/421575/Asp117_and_asp118_which_are/1'>Asp117 and Asp118 which are involved in Mg2+coordination</scene> <ref name="four">PMID:29438582</ref>.TM5–TM10 and loops C and D also play a role in the catalytic site and contain many polar and charged amino acids residues <ref name="one">PMID:29778697</ref>. Also, some polar and charged amino acids on TM9b and loop E are pointing toward the active site, making it even more hydrophilic.

In bacteria, MraYAA is in the form of a dimer, which is actually what researchers found in the first 3D structure of MraYAA <ref name="three"/>. Its N and the C termini are located on the periplasmic side. This protein is made of four extracellular loops, five cytoplasmic loops (named A,B, C, D and E) and ten transmembrane helices named TM1 to TM10. Though, TM9 is cleaved by a glycin residue into two helical segments named TM9a and TM9b. Furthermore, there is an additional helix between TM9b and TM10, which is only 11 residues long and is called TM9c. TM9c contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H324,325 and 326) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. They intereact with carbacaprazamycin, and also with other inhibitors such as [http://proteopedia.org/wiki/index.php/5ckr muraymycin D2 (MD2) ]. This small loop binds two Ni2+ ions, one on the two first histidines and the other one on the last one. Another part of this site is the residues corresponding to <scene name='42/421575/Asp117_and_asp118_which_are/1'>Asp117 and Asp118 which are involved in Mg2+coordination</scene> <ref name="four">PMID:29438582</ref>.TM5–TM10 and loops C and D also play a role in the catalytic site and contain many polar and charged amino acids residues <ref name="one">PMID:29778697</ref>. Also, some polar and charged amino acids on TM9b and loop E are pointing toward the active site, making it even more hydrophilic.

<scene name='42/421575/Carbacaprazamycin/1'>Carbacaprazamycin</scene> is made of uridine, 5-aminoribosyl, diazepanone, and aliphatic tail moieties. The diazepanone ring system makes relatively few interactions with the protein. Carbacapzazamycin contains an uridine binding pocket which is formed by amino acid residues in Loop C ( <scene name='42/421575/Binding_site/1'>G194, L195, and D196</scene>). This pocket is capped off by a π–π stacking interaction with <scene name='82/829360/F262/1'>F262</scene> in Loop D. <scene name='42/421575/Binding_site/1'>K70</scene> forms an additional hydrogen bond with the uracil moiety. Next to the uridine binding site, there is a second binding pocket lined with amino acid residues<scene name='42/421575/Binding_site/1'> T75, N190, D193, and G264</scene>, called the uridine-adjacent pocket. The 5-aminoribose moiety of carbacaprazamycin forms an extensive hydrogen bond network in the uridine-adjacent pocket. from those results we can observe that the uracil moiety binds to an enclosed pocket on the cytoplasmic face of MraY, while the ribosyl moiety is more solvent exposed <ref name="more1"/> <ref name="seven">PMID:31266949</ref>.

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@@ Line 22: / Line 22: @@
 == Asymmetric and biological unit ==
-The basal 3D scene shown on this page corresponds to the asymmetric unit, which contains 4 biological units of MraYAA (colors), which each of them is fused with the NB7 nanobody (teal). Mashalidis EH, Kaeser Bet al. , who solved this 3D structure, were screening antibodies. They determine that the presence of NB7 does not affect MraYAA enzymatic activity or inhibition by carbacaprazamycin <ref name="seven"/>.
+The basal 3D scene shown on this page corresponds to the asymmetric unit, which contains 4 <scene name='82/829360/4_biological_units/2'>biological units</scene> of MraYAA (colors), which each of them is fused with the NB7 nanobody (teal). Mashalidis EH, Kaeser Bet al. , who solved this 3D structure, were screening antibodies. They determine that the presence of NB7 does not affect MraYAA enzymatic activity or inhibition by carbacaprazamycin <ref name="seven"/>.
 == MraY-Carbacaprazamycin structure  ==
-In bacteria, MraYAA is in the form of a dimer, which actually what researchers found in the first 3D structure of MraYAA <ref name="three"/>. Its N and the C termini are located on the periplasmic side. This protein is made of four extracellular loops, five cytoplasmic loops (named A,B, C, D and E) and ten transmembrane helices named TM1 to TM10. Though, TM9 is cleaved by a glycin residue into two helical segments named TM9a and TM9b. Furthermore, there is an additional helix between TM9b and TM10, which is only 11 residues long and is called TM9c. TM9c contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H324,325 and 326) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. They intereact with carbacaprazamycin, and also with other inhibitors such as [http://proteopedia.org/wiki/index.php/5ckr muraymycin D2 (MD2) ]. This small loop binds two Ni2+ ions, one on the two first histidines and the other one on the last one. Another part of this site is the residues corresponding to <scene name='42/421575/Asp117_and_asp118_which_are/1'>Asp117 and Asp118   which are involved in Mg2+coordination</scene>  <ref name="four">PMID:29438582</ref>.TM5–TM10 and loops C and D also play a role in the catalytic site and contain many polar and charged amino acids residues <ref name="one">PMID:29778697</ref>.  Also, some polar and charged amino acids on TM9b and loop E are pointing toward the active site, making it even more hydrophilic.
+In bacteria, MraYAA is in the form of a dimer, which is actually what researchers found in the first 3D structure of MraYAA <ref name="three"/>. Its N and the C termini are located on the periplasmic side. This protein is made of four extracellular loops, five cytoplasmic loops (named A,B, C, D and E) and ten transmembrane helices named TM1 to TM10. Though, TM9 is cleaved by a glycin residue into two helical segments named TM9a and TM9b. Furthermore, there is an additional helix between TM9b and TM10, which is only 11 residues long and is called TM9c. TM9c contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H324,325 and 326) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. They intereact with carbacaprazamycin, and also with other inhibitors such as [http://proteopedia.org/wiki/index.php/5ckr muraymycin D2 (MD2) ]. This small loop binds two Ni2+ ions, one on the two first histidines and the other one on the last one. Another part of this site is the residues corresponding to <scene name='42/421575/Asp117_and_asp118_which_are/1'>Asp117 and Asp118   which are involved in Mg2+coordination</scene>  <ref name="four">PMID:29438582</ref>.TM5–TM10 and loops C and D also play a role in the catalytic site and contain many polar and charged amino acids residues <ref name="one">PMID:29778697</ref>.  Also, some polar and charged amino acids on TM9b and loop E are pointing toward the active site, making it even more hydrophilic.
 <scene name='42/421575/Carbacaprazamycin/1'>Carbacaprazamycin</scene> is made of uridine, 5-aminoribosyl, diazepanone, and aliphatic tail moieties. The diazepanone ring system makes relatively few interactions with the protein. Carbacapzazamycin contains an uridine binding pocket which is formed by amino acid residues in Loop C ( <scene name='42/421575/Binding_site/1'>G194, L195, and D196</scene>). This pocket is capped off by a π–π stacking interaction with <scene name='82/829360/F262/1'>F262</scene> in Loop D. <scene name='42/421575/Binding_site/1'>K70</scene> forms an additional hydrogen bond with the uracil moiety. Next to the uridine binding site, there is a second binding pocket lined with amino acid residues<scene name='42/421575/Binding_site/1'> T75, N190, D193, and G264</scene>, called the uridine-adjacent pocket. The 5-aminoribose moiety of carbacaprazamycin forms an extensive hydrogen bond network in the uridine-adjacent pocket. from those results we can observe that the uracil moiety binds to an enclosed pocket on the cytoplasmic face of MraY, while the ribosyl moiety is more solvent exposed <ref name="more1"/> <ref name="seven">PMID:31266949</ref>.