Sandbox Reserved 338: Difference between revisions

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==TreX==

TreX is an archaeal GDE from the species, [http://en.wikipedia.org/wiki/Sulfolobus ''Sulfolobus''] solfataricus <ref name="Woo" />. Interestingly, TreX exhibits 74% sequence similarity to the isoamylase from ''Sulfolobus acidocaldarium'', yet TreX itself reveals both α-1,6-glycosidase and α-1,4-transferase activity~~. It functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose <ref name="Woo" /> <ref name="oligomer"/>~~. Although TreX exhibits bifunctional activity, its catalytic region differs greatly from other glycogen debranching enzymes. For example, mammalian and yeast GDEs have distinct catalytic sites for the α-1,6-glycosidase activity and α-1,4-transferase activity. These sites are even located at different regions of the polypeptide. In TreX, however, both enzymatic rections take place within the same catalytic region <ref name="Woo" />.

TreX is an archaeal GDE from the species, [http://en.wikipedia.org/wiki/Sulfolobus ''Sulfolobus''] solfataricus <ref name="Woo" />. Interestingly, TreX exhibits 74% sequence similarity to the isoamylase from ''Sulfolobus acidocaldarium'', yet TreX itself reveals both α-1,6-glycosidase and α-1,4-transferase activity. Although TreX exhibits this bifunctional activity, its catalytic region differs greatly from other glycogen debranching enzymes. For example, mammalian and yeast GDEs have distinct catalytic sites for the α-1,6-glycosidase activity and α-1,4-transferase activity. These sites are even located at different regions of the polypeptide. In TreX, however, both enzymatic rections take place within the same catalytic region <ref name="Woo" />.

===Structure and Function===

TreX functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose <ref name="Woo" /> <ref name="oligomer"/>. The α-1,4-transferase activity is responsible for catalyzing the transfer of glucose residues from one 1,4-α-D-glucan branch to another, while the α-1,6-glycosidase activity is responsible for cleaving the lone glucose in an α-1,6-glycosidic linkage <ref name="lehninger">Nelson, D. and Cox, M. Lehninger Principles of Biochemistry (5th Ed.), W.H. Freeman and Company, New York (2008).</ref> <ref name="isoamylaseglucanotransferase"> PMID: 17485831 </ref>.

TreX is an oligomer, as it exists in a dimeric state and a tetrameric state, both of which exhibit different enzymatic activities. All subunits are identical, where the monomer contains a total of 612 amino acids <ref name="Woo" />. The polypeptide folds into two secondary structures, a β-sandwhich in the N terminal region, comprised of six β-strands and a (β/α)8 – barrel motif in the central domain, comprised of eight parallel α-strands which encircle eight parallel β-strands. The sequence composition of the TreX monomer exhibits a high degree of homology to the isoamylase debranching enzyme of Pseudomona, however the TreX monomer mainly deviates from this similarity in its substrate binding groove and the absence of a calcium ion ligand <ref name="Woo" />.

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[[Image: Glycogen_breakdown_3.png|thumb|Figure 1. Diagram illustrating the breakdown of glycogen near an (α1→6) branch point, and the steps where the α-1,6-glycosidase and the α-1,4-transferase activity of the glycogen debranching enzyme takes place. Diagram adapted from <ref name="lehninger"/>.]]

In human metabolism, glycogen breakdown involves several enzymes, two of which are glycogen phosphorylase and glycogen-debranching enzyme <ref name="lehninger"~~>Nelson, D. and Cox, M. Lehninger Principles of Biochemistry (5th Ed.), W.H. Freeman and Company, New York (2008).<~~/~~ref~~>. Glycogen phosphorylase is responsible for the successive removal of glucose 1-phosphate molecules at the non reducing ends of glycogen branches <ref name="lehninger"/>. However, this enzyme’s activity ceases when it has reached a point four glucose residues away from an (α1→6) branch point. Upon this, the GDE takes over and catalyzes the transfer of three branched glucose units to the nonreducing end of another branch to yield an (α1→4) linkage. The α-1,6-glycosidase activity of the GDE liberates the non-transferred glucose unit involved in a (α1→6) bond <ref name="lehninger"/>.

In human metabolism, glycogen breakdown involves several enzymes, two of which are glycogen phosphorylase and glycogen-debranching enzyme <ref name="lehninger"/>. Glycogen phosphorylase is responsible for the successive removal of glucose 1-phosphate molecules at the non reducing ends of glycogen branches <ref name="lehninger"/>. However, this enzyme’s activity ceases when it has reached a point four glucose residues away from an (α1→6) branch point. Upon this, the GDE takes over and catalyzes the transfer of three branched glucose units to the nonreducing end of another branch to yield an (α1→4) linkage. The α-1,6-glycosidase activity of the GDE liberates the non-transferred glucose unit involved in a (α1→6) bond <ref name="lehninger"/>.

Although TreX is structurally different from the yeast and mammalian GDE, it does however share functional similarities, and therefore a general mammalian GDE mechanism is shown. In both species the GDE catalyzes an intermolecular transfer of glucose polymers from one 1,4-α-D-glucan branch to another 1,4-α-D-glucan branch nearby, In addition, both enzymes carry out the hydrolysis of an α-1,6-glycosidic linkage <ref name="isoamylaseglucanotransferase"~~> PMID: 17485831 <~~/~~ref~~>. TreX does however show high specificity for side chains which are composed of 6 or more glucose residues <ref name="oligomer"> Park JT, Park HS, Kang HK, Hong JS, Cha H, Woo EJ, Kim JW, Kim MJ, Boos W, Lee S, Park KH (2008). "Oligomeric and functional properties of a debranching enzyme (TreX) from the archaeon Sulfobus solfataricus P2.". Biocatalysis and Biotransformation 26: 76–85.</ref>.

Although TreX is structurally different from the yeast and mammalian GDE, it does however share functional similarities, and therefore a general mammalian GDE mechanism is shown. In both species the GDE catalyzes an intermolecular transfer of glucose polymers from one 1,4-α-D-glucan branch to another 1,4-α-D-glucan branch nearby, In addition, both enzymes carry out the hydrolysis of an α-1,6-glycosidic linkage <ref name="isoamylaseglucanotransferase"/>. TreX does however show high specificity for side chains which are composed of 6 or more glucose residues <ref name="oligomer"> Park JT, Park HS, Kang HK, Hong JS, Cha H, Woo EJ, Kim JW, Kim MJ, Boos W, Lee S, Park KH (2008). "Oligomeric and functional properties of a debranching enzyme (TreX) from the archaeon Sulfobus solfataricus P2.". Biocatalysis and Biotransformation 26: 76–85.</ref>.

==References==

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@@ Line 10: / Line 10: @@
 ==TreX==
-TreX is an archaeal GDE from the species, [http://en.wikipedia.org/wiki/Sulfolobus ''Sulfolobus''] solfataricus <ref name="Woo" />. Interestingly, TreX exhibits 74% sequence similarity to the isoamylase from ''Sulfolobus acidocaldarium'', yet TreX itself reveals both α-1,6-glycosidase and α-1,4-transferase activity. It functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose <ref name="Woo" /> <ref name="oligomer"/>. Although TreX exhibits bifunctional activity, its catalytic region differs greatly from other glycogen debranching enzymes. For example, mammalian and yeast GDEs have distinct catalytic sites for the α-1,6-glycosidase activity and α-1,4-transferase activity. These sites are even located at different regions of the polypeptide. In TreX, however, both enzymatic rections take place within the same catalytic region <ref name="Woo" />.
+TreX is an archaeal GDE from the species, [http://en.wikipedia.org/wiki/Sulfolobus ''Sulfolobus''] solfataricus <ref name="Woo" />. Interestingly, TreX exhibits 74% sequence similarity to the isoamylase from ''Sulfolobus acidocaldarium'', yet TreX itself reveals both α-1,6-glycosidase and α-1,4-transferase activity. Although TreX exhibits this bifunctional activity, its catalytic region differs greatly from other glycogen debranching enzymes. For example, mammalian and yeast GDEs have distinct catalytic sites for the α-1,6-glycosidase activity and α-1,4-transferase activity. These sites are even located at different regions of the polypeptide. In TreX, however, both enzymatic rections take place within the same catalytic region <ref name="Woo" />.
 ===Structure and Function===
 <Structure load='2vnc' size='300' frame='true' align='right' scene='Sandbox_Reserved_338/2vnc/1' />
+TreX functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose <ref name="Woo" /> <ref name="oligomer"/>. The α-1,4-transferase activity is responsible for catalyzing the transfer of glucose residues from one 1,4-α-D-glucan branch to another, while the α-1,6-glycosidase activity is responsible for cleaving the lone glucose in an α-1,6-glycosidic linkage <ref name="lehninger">Nelson, D. and Cox, M. Lehninger Principles of Biochemistry (5th Ed.), W.H. Freeman and Company, New York (2008).</ref> <ref name="isoamylaseglucanotransferase"> PMID: 17485831 </ref>.
 TreX is an oligomer, as it exists in a dimeric state and a tetrameric state, both of which exhibit different enzymatic activities. All subunits are identical, where the monomer contains a total of 612 amino acids <ref name="Woo" />.  The polypeptide folds into two secondary structures, a β-sandwhich in the N terminal region, comprised of six β-strands and a (β/α)8 – barrel motif in the central domain, comprised of eight parallel α-strands which encircle eight parallel β-strands. The sequence composition of the TreX monomer exhibits a high degree of homology to the isoamylase debranching enzyme of Pseudomona, however the TreX monomer mainly deviates from this similarity in its substrate binding groove and the absence of a calcium ion ligand <ref name="Woo" />.
@@ Line 28: / Line 30: @@
 [[Image: Glycogen_breakdown_3.png|thumb|Figure 1. Diagram illustrating the breakdown of glycogen near an (α1→6) branch point, and the steps where the α-1,6-glycosidase and the α-1,4-transferase activity of the glycogen debranching enzyme takes place. Diagram adapted from <ref name="lehninger"/>.]]
-In human metabolism, glycogen breakdown involves several enzymes, two of which are glycogen phosphorylase and glycogen-debranching enzyme <ref name="lehninger">Nelson, D. and Cox, M. Lehninger Principles of Biochemistry (5th Ed.), W.H. Freeman and Company, New York (2008).</ref>. Glycogen phosphorylase is responsible for the successive removal of glucose 1-phosphate molecules at the non reducing ends of glycogen branches <ref name="lehninger"/>. However, this enzyme’s activity ceases when it has reached a point four glucose residues away from an (α1→6) branch point. Upon this, the GDE takes over and catalyzes the transfer of three branched glucose units to the nonreducing end of another branch to yield an (α1→4) linkage. The α-1,6-glycosidase activity of the GDE liberates the non-transferred glucose unit involved in a (α1→6) bond <ref name="lehninger"/>.
+In human metabolism, glycogen breakdown involves several enzymes, two of which are glycogen phosphorylase and glycogen-debranching enzyme <ref name="lehninger"/>. Glycogen phosphorylase is responsible for the successive removal of glucose 1-phosphate molecules at the non reducing ends of glycogen branches <ref name="lehninger"/>. However, this enzyme’s activity ceases when it has reached a point four glucose residues away from an (α1→6) branch point. Upon this, the GDE takes over and catalyzes the transfer of three branched glucose units to the nonreducing end of another branch to yield an (α1→4) linkage. The α-1,6-glycosidase activity of the GDE liberates the non-transferred glucose unit involved in a (α1→6) bond <ref name="lehninger"/>.
-Although TreX is structurally different from the yeast and mammalian GDE, it does however share functional similarities, and therefore a general mammalian GDE mechanism is shown. In both species the  GDE catalyzes an intermolecular transfer  of glucose polymers from one 1,4-α-D-glucan branch to another 1,4-α-D-glucan branch nearby, In addition, both enzymes carry out the hydrolysis of an α-1,6-glycosidic linkage <ref name="isoamylaseglucanotransferase"> PMID: 17485831 </ref>. TreX does however show high specificity for side chains which are composed of 6 or more glucose residues <ref name="oligomer"> Park JT, Park HS, Kang HK, Hong JS, Cha H, Woo EJ, Kim JW, Kim MJ, Boos W, Lee S, Park KH (2008). "Oligomeric and functional properties of a debranching enzyme (TreX) from the archaeon Sulfobus solfataricus P2.". Biocatalysis and Biotransformation 26: 76–85.</ref>.
+Although TreX is structurally different from the yeast and mammalian GDE, it does however share functional similarities, and therefore a general mammalian GDE mechanism is shown. In both species the  GDE catalyzes an intermolecular transfer  of glucose polymers from one 1,4-α-D-glucan branch to another 1,4-α-D-glucan branch nearby, In addition, both enzymes carry out the hydrolysis of an α-1,6-glycosidic linkage <ref name="isoamylaseglucanotransferase"/>. TreX does however show high specificity for side chains which are composed of 6 or more glucose residues <ref name="oligomer"> Park JT, Park HS, Kang HK, Hong JS, Cha H, Woo EJ, Kim JW, Kim MJ, Boos W, Lee S, Park KH (2008). "Oligomeric and functional properties of a debranching enzyme (TreX) from the archaeon Sulfobus solfataricus P2.". Biocatalysis and Biotransformation 26: 76–85.</ref>.
 ==References==
 <references/>