Sandbox Reserved 338: Difference between revisions

Line 24:

The active site of the TreX dimer contains three important catalytic residues <scene name='Sandbox_Reserved_338/2vnc/5'>(Asp 363, Glu 399, and Asp 471)</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 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 <scene name='Sandbox_Reserved_338/228_238/1'>(aa 228-238)</scene> 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 <scene name='Sandbox_Reserved_338/Lid1/2'>(aa 92-97)</scene> and lid 2 <scene name='Sandbox_Reserved_338/315-322/1'>(aa 315-322)</scene>, 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 <scene name='Sandbox_Reserved_338/2vnc/6'>(aa 399 – 416)</scene> 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" />.

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 <scene name='Sandbox_Reserved_338/Lid1/2'>(aa 92-97)</scene> and lid 2 <scene name='Sandbox_Reserved_338/315-322/1'>(aa 315-322)</scene>, 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 <scene name='Sandbox_Reserved_338/2vnc/6'>(aa 399-416)</scene> 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" />.

===Mechanism===

Sandbox Reserved 338: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 24: / Line 24: @@
 The active site of the TreX dimer contains three important catalytic residues <scene name='Sandbox_Reserved_338/2vnc/5'>(Asp 363, Glu 399, and Asp 471)</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 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 <scene name='Sandbox_Reserved_338/228_238/1'>(aa 228-238)</scene> 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 <scene name='Sandbox_Reserved_338/Lid1/2'>(aa 92-97)</scene> and lid 2 <scene name='Sandbox_Reserved_338/315-322/1'>(aa 315-322)</scene>, 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 <scene name='Sandbox_Reserved_338/2vnc/6'>(aa 399 – 416)</scene> 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" />.
+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 <scene name='Sandbox_Reserved_338/Lid1/2'>(aa 92-97)</scene> and lid 2 <scene name='Sandbox_Reserved_338/315-322/1'>(aa 315-322)</scene>, 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 <scene name='Sandbox_Reserved_338/2vnc/6'>(aa 399-416)</scene> 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" />.
 ===Mechanism===