2f6d: Difference between revisions

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Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose

OverviewOverview

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.

About this StructureAbout this Structure

2F6D is a Single protein structure of sequence from Saccharomycopsis fibuligera with , and as ligands. Active as Glucan 1,4-alpha-glucosidase, with EC number 3.2.1.3 Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:2f6d.gif|left|200px]]<br /><applet load="2f6d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2f6d.gif|left|200px]]<br /><applet load="2f6d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2f6d, resolution 1.60&Aring;" />
 '''Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-F6D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomycopsis_fibuligera Saccharomycopsis fibuligera] with ACR, PO4 and NA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2F6D OCA].
+F6D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomycopsis_fibuligera Saccharomycopsis fibuligera] with <scene name='pdbligand=ACR:'>ACR</scene>, <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6D OCA].
 ==Reference==
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 [[Category: Sevcik, J.]]
 [[Category: Solovicova, A.]]
-[[Category: Wilson, K.S.]]
+[[Category: Wilson, K S.]]
 [[Category: ACR]]
 [[Category: NA]]
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 [[Category: sugar tongs]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:23:27 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:18:10 2008''