1dog
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(New page: 200px<br /> <applet load="1dog" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dog, resolution 2.3Å" /> '''REFINED STRUCTURE FO...)
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Revision as of 06:52, 18 November 2007
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REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION
Overview
The three-dimensional structure of the complex of 1-deoxynojirimycin with, glucoamylase II-(471) from Aspergillus awamori var. X100 has been, determined to 2.4-A resolution. The model includes residues corresponding, to residues 1-471 of glucoamylase I from Aspergillus niger, two molecules, of bound 1-deoxynojirimycin and 605 sites for water molecules. The, crystallographic R factor from refinement is 0.119, and the, root-mean-squared deviation in bond distances is 0.012 A. The inhibitor, complex confirms the location of the active site in the packing void of, the alpha/alpha-barrel as proposed by Aleshin et al. [Aleshin, A., Golubev, A., Firsov, L., & Honzatko, R. B. (1992) J. Biol. Chem. 267, 19291-19298]. One inhibitor molecule is associated with strong electron, density and represents the principal site of interaction of, 1-deoxynojirimycin with the enzyme. The other 1-deoxynojirimycin molecule, is associated with weak electron density and therefore, probably, represents a binding site of low affinity. Interactions of, 1-deoxynojirimycin with the enzyme at its principal site involve Arg 45, Asp 55, Arg 305, and carbonyl 177. In addition, a water molecule (water, 500) hydrogen bonds to Glu 400 and the 6-hydroxyl of 1-deoxynojirimycin, and is at an approximate distance of 3.3 A from the "anomeric" carbon of, the inhibitor. The structural arrangement of functional groups near the, inhibitor molecule suggests that Glu 179 is a catalytic acid, Glu 400 a, catalytic base, and water 500 the attacking nucleophile in the hydrolysis, of maltooligosaccharides. The relevance of the X-ray work to proposed, mechanisms of enzymatic hydrolysis of oligosaccharides is discussed.
About this Structure
1DOG is a Single protein structure of sequence from Aspergillus awamori with MAN and NOJ as ligands. The following page contains interesting information on the relation of 1DOG with [Alpha-amylase]. Active as Glucan 1,4-alpha-glucosidase, with EC number 3.2.1.3 Full crystallographic information is available from OCA.
Reference
Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution., Harris EM, Aleshin AE, Firsov LM, Honzatko RB, Biochemistry. 1993 Feb 16;32(6):1618-26. PMID:8431441
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