2f6d
From Proteopedia
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|PDB= 2f6d |SIZE=350|CAPTION= <scene name='initialview01'>2f6d</scene>, resolution 1.60Å | |PDB= 2f6d |SIZE=350|CAPTION= <scene name='initialview01'>2f6d</scene>, resolution 1.60Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ACR:ACARBOSE'>ACR</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ACR:ACARBOSE'>ACR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= GLU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4944 Saccharomycopsis fibuligera]) | |GENE= GLU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4944 Saccharomycopsis fibuligera]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1ayx|1AYX]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f6d OCA], [http://www.ebi.ac.uk/pdbsum/2f6d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f6d RCSB]</span> | ||
}} | }} | ||
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[[Category: Solovicova, A.]] | [[Category: Solovicova, A.]] | ||
[[Category: Wilson, K S.]] | [[Category: Wilson, K S.]] | ||
| - | [[Category: ACR]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: PO4]] | ||
[[Category: (alpha-alpha)6 barrel]] | [[Category: (alpha-alpha)6 barrel]] | ||
[[Category: protein-acarbose complex]] | [[Category: protein-acarbose complex]] | ||
[[Category: sugar tong]] | [[Category: sugar tong]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:58:34 2008'' |
Revision as of 23:58, 30 March 2008
| |||||||
| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | GLU1 (Saccharomycopsis fibuligera) | ||||||
| Activity: | Glucan 1,4-alpha-glucosidase, with EC number 3.2.1.3 | ||||||
| Related: | 1AYX
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose
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.
About this Structure
2F6D is a Single protein structure of sequence from Saccharomycopsis fibuligera. Full crystallographic information is available from OCA.
Reference
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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