2f6d: Difference between revisions
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==== | ==Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose== | ||
<StructureSection load='2f6d' size='340' side='right'caption='[[2f6d]]' scene=''> | <StructureSection load='2f6d' size='340' side='right'caption='[[2f6d]], [[Resolution|resolution]] 1.60Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[2f6d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_36309 Atcc 36309]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F6D FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f6d OCA], [https://pdbe.org/2f6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f6d RCSB], [https://www.ebi.ac.uk/pdbsum/2f6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f6d 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ayx|1ayx]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLU1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4944 ATCC 36309])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f6d OCA], [https://pdbe.org/2f6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f6d RCSB], [https://www.ebi.ac.uk/pdbsum/2f6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f6d ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f6d ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f6d ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Most glucoamylases (alpha-1,4-D-glucan glucohydrolase, EC 3.2.1.3) have structures consisting of both a catalytic and a starch binding domain. The structure of a glucoamylase from Saccharomycopsis fibuligera HUT 7212 (Glu), determined a few years ago, consists of a single catalytic domain. The structure of this enzyme with the resolution extended to 1.1 A and that of the enzyme-acarbose complex at 1.6 A resolution are presented here. The structure at atomic resolution, besides its high accuracy, shows clearly the influence of cryo-cooling, which is manifested in shrinkage of the molecule and lowering the volume of the unit cell. In the structure of the complex, two acarbose molecules are bound, one at the active site and the second at a site remote from the active site, curved around Tyr464 which resembles the inhibitor molecule in the 'sugar tongs' surface binding site in the structure of barley alpha-amylase isozyme 1 complexed with a thiomalto-oligosaccharide. Based on the close similarity in sequence of glucoamylase Glu, which does not degrade raw starch, to that of glucoamylase (Glm) from S. fibuligera IFO 0111, a raw starch-degrading enzyme, it is reasonable to expect the presence of the remote starch binding site at structurally equivalent positions in both enzymes. We propose the role of this site is to fix the enzyme onto the surface of a starch granule while the active site degrades the polysaccharide. This hypothesis is verified here by the preparation of mutants of glucoamylases Glu and Glm. | |||
Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.,Sevcik J, Hostinova E, Solovicova A, Gasperik J, Dauter Z, Wilson KS FEBS J. 2006 May;273(10):2161-71. PMID:16649993<ref>PMID:16649993</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2f6d" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 36309]] | |||
[[Category: Glucan 1,4-alpha-glucosidase]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Z- | [[Category: Dauter, Z]] | ||
[[Category: Gasperik, J]] | |||
[[Category: Hostinova, E]] | |||
[[Category: Sevcik, J]] | |||
[[Category: Solovicova, A]] | |||
[[Category: Wilson, K S]] | |||
[[Category: Hydrolase]] | |||
[[Category: Protein-acarbose complex]] | |||
[[Category: Sugar tong]] | |||
Revision as of 12:18, 24 February 2021
Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarboseStructure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMost glucoamylases (alpha-1,4-D-glucan glucohydrolase, EC 3.2.1.3) have structures consisting of both a catalytic and a starch binding domain. The structure of a glucoamylase from Saccharomycopsis fibuligera HUT 7212 (Glu), determined a few years ago, consists of a single catalytic domain. The structure of this enzyme with the resolution extended to 1.1 A and that of the enzyme-acarbose complex at 1.6 A resolution are presented here. The structure at atomic resolution, besides its high accuracy, shows clearly the influence of cryo-cooling, which is manifested in shrinkage of the molecule and lowering the volume of the unit cell. In the structure of the complex, two acarbose molecules are bound, one at the active site and the second at a site remote from the active site, curved around Tyr464 which resembles the inhibitor molecule in the 'sugar tongs' surface binding site in the structure of barley alpha-amylase isozyme 1 complexed with a thiomalto-oligosaccharide. Based on the close similarity in sequence of glucoamylase Glu, which does not degrade raw starch, to that of glucoamylase (Glm) from S. fibuligera IFO 0111, a raw starch-degrading enzyme, it is reasonable to expect the presence of the remote starch binding site at structurally equivalent positions in both enzymes. We propose the role of this site is to fix the enzyme onto the surface of a starch granule while the active site degrades the polysaccharide. This hypothesis is verified here by the preparation of mutants of glucoamylases Glu and Glm. Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.,Sevcik J, Hostinova E, Solovicova A, Gasperik J, Dauter Z, Wilson KS FEBS J. 2006 May;273(10):2161-71. PMID:16649993[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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