Sandbox Reserved 338: Difference between revisions

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In the dimeric form, the individual subunits are adjacent to each other, where both of the active sites face the same side <ref name="Woo" />. In the tetrameric form, two of the associated dimers face each other so as to position the substrate binding sites to the inside of the tetramer, facing each other with a slight offset <ref name="Woo" />. Unlike other GDEs, TreX portrays different enzymatic activities in correlation to its oligomeric state. The dimeric form is predominantly associated with α-1,6-glycosidase, whereas the tetratmeic form is associated with α-1,4-transferase activity <ref name="Woo" />.

The active site of the TreX dimer contains three important catalytic residues (Asp363, Glu399, and Asp471) situated at the bottom of the active site cleft. The dimer active site exhibits a buried interface of 1523 Å, and a total of 6 subsites, where subsite 1 contains the NYWDYDP motif important which facilitates substrate interactions of the glucose rings. One of the interesting features which separate TreX from similar isoamylases and pullulanases, it the presence of a helix α4 loop (aa 228-238) situated at the bottom of the substrate binding groove. It is suggested that this helix α4 loop may provide a stable binding region for branched substrates with long chains, and therefore increase the activity of this GDE <ref name="Woo" />.

The active site of the TreX dimer contains three important catalytic residues <scene name='Sandbox_Reserved_338/3res/1'>(Asp363, Glu399, and Asp471)</scene> situated at the bottom of the active site cleft. The dimer active site exhibits a buried interface of 1523 Å, and a total of 6 subsites, where subsite 1 contains the NYWDYDP motif important which facilitates substrate interactions of the glucose rings. One of the interesting features which separate TreX from similar isoamylases and pullulanases, it the presence of a helix α4 loop (aa 228-238) situated at the bottom of the substrate binding groove. It is suggested that this helix α4 loop may provide a stable binding region for branched substrates with long chains, and therefore increase the activity of this GDE <ref name="Woo" />.

Upon tetramerization, TreX’s active site undergoes a substantial change in conformation, and thus displays both structural and functional differences when compared to the TreX dimer and even to other GDEs. Studies have revealed that the TreX tetramer displays a 4-fold increase in catalytic activity, when compared to the dimer. It is postulated that the conformational change in the active site only occurs in the presence of branched substrates with long chains, such as glycogen, because it establishes an ideal binding site for these types of substrates. To illustrate, the TreX tetramer is composed of two dimers, whose active sites face each other with a slight offset. As a consequence, particular regions of one dimer, such as lid 1(aa 92-97) and lid 2 (aa 315-322), are situated in the active site of the other dimer. This arrangement of the dimers’ structural lids results in the formation of a channel like cavity and a conformational change in a loop (aa 399 – 416) situated within the active site. The two lid structures have been greatly associated with increased α-1,4-transferase activity in TreX, and interestingly, their conformation exhibits structural similarity to that of other glucosyltransferase enzymes, which also encompass structural lids close to their active sites. Thus, the implicated function of the lid structures during catalysis is to interact with acceptor molecules, such as glycogen, and provide stability to the complex, so that glycogen may be broken down into long maltooligosacchardies <ref name="Woo" />.

Sandbox Reserved 338: Difference between revisions

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 In the dimeric form, the individual subunits are adjacent to each other, where both of the active sites face the same side <ref name="Woo" />. In the tetrameric form, two of the associated dimers face each other so as to position the substrate binding sites to the inside of the tetramer, facing each other with a slight offset <ref name="Woo" />. Unlike other GDEs, TreX portrays different enzymatic activities in correlation to its oligomeric state. The dimeric form is predominantly associated with α-1,6-glycosidase, whereas the tetratmeic form is associated with α-1,4-transferase activity <ref name="Woo" />.
-The active site of the TreX dimer contains three important catalytic residues (Asp<sup>363</sup>, Glu<sup>399</sup>, and Asp<sup>471</sup>) situated at the bottom of the active site cleft.  The dimer active site exhibits a buried interface of 1523 Å, and a total of 6 subsites, where subsite 1 contains the NYWDYDP motif important which facilitates substrate interactions of the glucose rings. One of the interesting features which separate TreX from similar isoamylases and pullulanases, it the presence of a helix α4 loop (aa 228-238) situated at the bottom of the substrate binding groove.  It is suggested that this helix α4 loop may provide a stable binding region for branched substrates with long chains, and therefore increase the activity of this GDE <ref name="Woo" />.
+The active site of the TreX dimer contains three important catalytic residues <scene name='Sandbox_Reserved_338/3res/1'>(Asp<sup>363</sup>, Glu<sup>399</sup>, and Asp<sup>471</sup>)</scene> situated at the bottom of the active site cleft.  The dimer active site exhibits a buried interface of 1523 Å, and a total of 6 subsites, where subsite 1 contains the NYWDYDP motif important which facilitates substrate interactions of the glucose rings. One of the interesting features which separate TreX from similar isoamylases and pullulanases, it the presence of a helix α4 loop (aa 228-238) situated at the bottom of the substrate binding groove.  It is suggested that this helix α4 loop may provide a stable binding region for branched substrates with long chains, and therefore increase the activity of this GDE <ref name="Woo" />.
 Upon tetramerization, TreX’s active site undergoes a substantial change in conformation, and thus displays both structural and functional differences when compared to the TreX dimer and even to other GDEs. Studies have revealed that the TreX tetramer displays a 4-fold increase in catalytic activity, when compared to the dimer. It is postulated that the conformational change in the active site only occurs in the presence of branched substrates with long chains, such as glycogen, because it establishes an ideal binding site for these types of substrates. To illustrate, the TreX tetramer is composed of two dimers, whose active sites face each other with a slight offset. As a consequence, particular regions of one dimer, such as lid 1(aa 92-97) and lid 2 (aa 315-322), are situated in the active site of the other dimer. This arrangement of the dimers’ structural lids results in the formation of a channel like cavity and a conformational change in a loop (aa 399 – 416) situated within the active site. The two lid structures have been greatly associated with increased α-1,4-transferase activity in TreX, and interestingly, their conformation exhibits structural similarity to that of other glucosyltransferase enzymes, which also encompass structural lids close to their active sites. Thus, the implicated function of the lid structures during catalysis is to interact with acceptor molecules, such as glycogen, and provide stability to the complex, so that glycogen may be broken down into long maltooligosacchardies <ref name="Woo" />.