1agm: Difference between revisions

Revision as of 12:44, 21 February 2008

REFINED STRUCTURE FOR THE COMPLEX OF ACARBOSE WITH GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100 TO 2.4 ANGSTROMS RESOLUTION

OverviewOverview

The three-dimensional structure of the pseudotetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to 1-471 of glucoamylase I from Aspergillus niger, a single molecule of bound acarbose, and 535 sites for water molecules. The crystallographic R factor from refinement is 0.124, and the root-mean-squared deviation in bond distances is 0.013 A. Electron density for a single molecule of bound acarbose defines what may be the first four subsites in the binding of extended maltooligosaccharides. Hydrogen bonds between acarbose and the enzyme involve Arg54, Asp55, Arg305, carbonyl177, main chain amide121, Glu179, Glu180, and carbonyl179. Glu179 forms a salt link to the imino linkage between the first and second residues of acarbose. This buried salt link probably contributes significantly to the unusually tight association (Kd approximately 10(-12) M) of acarbose with glucoamylase. In addition, a significant hydrophobic contact between the third residue of acarbose and the side chain of Trp120 distorts the three-center angle of the glucosidic linkage between the second and third residues of acarbose. A water molecule (water500) hydrogen bonds to Glu400 and the 6-hydroxyl of the valienamine moiety of acarbose and is at an approximate distance of 3.7 A from the "anomeric" carbon of the inhibitor. The relevance of the acarbose-glucoamylase complex to the mechanism of enzymic hydrolysis of oligosaccharides is discussed.

About this StructureAbout this Structure

1AGM is a Single protein structure of sequence from Aspergillus awamori with as ligand. Active as Glucan 1,4-alpha-glucosidase, with EC number 3.2.1.3 Full crystallographic information is available from OCA.

ReferenceReference

Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution., Aleshin AE, Firsov LM, Honzatko RB, J Biol Chem. 1994 Jun 3;269(22):15631-9. PMID:8195212

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-[[Image:1agm.gif|left|200px]]<br /><applet load="1agm" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1agm.gif|left|200px]]<br /><applet load="1agm" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1agm, resolution 2.30&Aring;" />
 '''REFINED STRUCTURE FOR THE COMPLEX OF ACARBOSE WITH GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100 TO 2.4 ANGSTROMS RESOLUTION'''<br />
 ==Overview==
-The three-dimensional structure of the pseudotetrasaccharide acarbose, complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has, been determined to 2.4-A resolution. The model includes residues, corresponding to 1-471 of glucoamylase I from Aspergillus niger, a single, molecule of bound acarbose, and 535 sites for water molecules. The, crystallographic R factor from refinement is 0.124, and the, root-mean-squared deviation in bond distances is 0.013 A. Electron density, for a single molecule of bound acarbose defines what may be the first four, subsites in the binding of extended maltooligosaccharides. Hydrogen bonds, between acarbose and the enzyme involve Arg54, Asp55, Arg305, carbonyl177, main chain amide121, Glu179, Glu180, and carbonyl179. Glu179 forms a salt, link to the imino linkage between the first and second residues of, acarbose. This buried salt link probably contributes significantly to the, unusually tight association (Kd approximately 10(-12) M) of acarbose with, glucoamylase. In addition, a significant hydrophobic contact between the, third residue of acarbose and the side chain of Trp120 distorts the, three-center angle of the glucosidic linkage between the second and third, residues of acarbose. A water molecule (water500) hydrogen bonds to Glu400, and the 6-hydroxyl of the valienamine moiety of acarbose and is at an, approximate distance of 3.7 A from the "anomeric" carbon of the inhibitor., The relevance of the acarbose-glucoamylase complex to the mechanism of, enzymic hydrolysis of oligosaccharides is discussed.
+The three-dimensional structure of the pseudotetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to 1-471 of glucoamylase I from Aspergillus niger, a single molecule of bound acarbose, and 535 sites for water molecules. The crystallographic R factor from refinement is 0.124, and the root-mean-squared deviation in bond distances is 0.013 A. Electron density for a single molecule of bound acarbose defines what may be the first four subsites in the binding of extended maltooligosaccharides. Hydrogen bonds between acarbose and the enzyme involve Arg54, Asp55, Arg305, carbonyl177, main chain amide121, Glu179, Glu180, and carbonyl179. Glu179 forms a salt link to the imino linkage between the first and second residues of acarbose. This buried salt link probably contributes significantly to the unusually tight association (Kd approximately 10(-12) M) of acarbose with glucoamylase. In addition, a significant hydrophobic contact between the third residue of acarbose and the side chain of Trp120 distorts the three-center angle of the glucosidic linkage between the second and third residues of acarbose. A water molecule (water500) hydrogen bonds to Glu400 and the 6-hydroxyl of the valienamine moiety of acarbose and is at an approximate distance of 3.7 A from the "anomeric" carbon of the inhibitor. The relevance of the acarbose-glucoamylase complex to the mechanism of enzymic hydrolysis of oligosaccharides is discussed.
 ==About this Structure==
-AGM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori] with MAN as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1AGM OCA].
+AGM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori] with <scene name='pdbligand=MAN:'>MAN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1AGM OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Glucan 1,4-alpha-glucosidase]]
 [[Category: Single protein]]
-[[Category: Aleshin, A.E.]]
+[[Category: Aleshin, A E.]]
-[[Category: Firsov, L.M.]]
+[[Category: Firsov, L M.]]
-[[Category: Honzatko, R.B.]]
+[[Category: Honzatko, R B.]]
 [[Category: MAN]]
 [[Category: hydrolase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:50:08 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:44:17 2008''