Sandbox Reserved 110: Difference between revisions
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== Structure == | == Structure == | ||
MraY is a '''membrane-bound enzyme''', for which the 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 … 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. This helix contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H290, 291 and 292) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. For example; they interact with tunicamycin and 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 Asp117 and Asp118 which are involved in Mg2+coordination <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 <ref name="four">PMID:29438582</ref>. | MraY is a '''membrane-bound enzyme''', for which the 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 … 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. This helix contains a <scene name='42/421575/His_triad/1'>HHH motif</scene> (H290, 291 and 292) which plays a role in the enzyme’s substrat selectivity and is a part of the catalytic site <ref name="one">PMID:29778697</ref>. For example; they interact with tunicamycin and 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 <ref name="four">PMID:29438582</ref>. | ||
<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='42/421575/Binding_site/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 <ref name="seven">PMID:31266949</ref>. | <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='42/421575/Binding_site/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 <ref name="seven">PMID:31266949</ref>. | ||
Revision as of 15:17, 16 January 2020
| This Sandbox is Reserved from May 18 through July 31, 2015 for use in the workshop Protein 3D Structure Visualization & Structural Bioinformatics taught by Eric Martz and Fadel Samatey at the Okinawa Institute of Science and Technology, Japan. This reservation includes Sandbox Reserved 101 through Sandbox Reserved 150. See Workshops.MolviZ.Org. |
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Crystal structure of MraY bound to carbacaprazamycin
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