6lx2: Difference between revisions
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==Potato D-enzyme complexed with CA26== | ==Potato D-enzyme complexed with CA26== | ||
<StructureSection load='6lx2' size='340' side='right'caption='[[6lx2]]' scene=''> | <StructureSection load='6lx2' size='340' side='right'caption='[[6lx2]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LX2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LX2 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6lx2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Potato Potato]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LX2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LX2 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lx2 OCA], [http://pdbe.org/6lx2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lx2 RCSB], [http://www.ebi.ac.uk/pdbsum/6lx2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lx2 ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G4D:4-DEOXY-ALPHA-D-GLUCOSE'>G4D</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x1n|1x1n]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPEP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4113 Potato])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-alpha-glucanotransferase 4-alpha-glucanotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.25 2.4.1.25] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lx2 OCA], [http://pdbe.org/6lx2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lx2 RCSB], [http://www.ebi.ac.uk/pdbsum/6lx2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lx2 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/DPEP_SOLTU DPEP_SOLTU]] May act during starch breakdown to convert small oligosaccharides into larger molecules upon which starch phosphorylase can act, or may change the structure of starch molecules and grain architecture by modifying chain length, or may generate from starch and glucose oligosaccharides which can serve either as primers for new starch phosphoenzyme. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Starch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of alpha-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops. | |||
Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato.,Imamura K, Matsuura T, Nakagawa A, Kitamura S, Kusunoki M, Takaha T, Unno H Protein Sci. 2020 Aug 18. doi: 10.1002/pro.3932. PMID:32808707<ref>PMID:32808707</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6lx2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: 4-alpha-glucanotransferase]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Imamura K]] | [[Category: Potato]] | ||
[[Category: Unno H]] | [[Category: Imamura, K]] | ||
[[Category: Unno, H]] | |||
[[Category: Cycloamylose]] | |||
[[Category: D-enzyme]] | |||
[[Category: Disproportionating enzyme]] | |||
[[Category: Plant protein]] | |||
[[Category: Solanum tuberosum]] | |||
[[Category: Transferase]] | |||
Revision as of 14:22, 23 September 2020
Potato D-enzyme complexed with CA26Potato D-enzyme complexed with CA26
Structural highlights
Function[DPEP_SOLTU] May act during starch breakdown to convert small oligosaccharides into larger molecules upon which starch phosphorylase can act, or may change the structure of starch molecules and grain architecture by modifying chain length, or may generate from starch and glucose oligosaccharides which can serve either as primers for new starch phosphoenzyme. Publication Abstract from PubMedStarch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of alpha-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops. Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato.,Imamura K, Matsuura T, Nakagawa A, Kitamura S, Kusunoki M, Takaha T, Unno H Protein Sci. 2020 Aug 18. doi: 10.1002/pro.3932. PMID:32808707[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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