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| ==Overview==
| | {{ABSTRACT_8431441}} |
| 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.
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| ==About this Structure== | | ==About this Structure== |
| 1DOG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. The following page contains interesting information on the relation of 1DOG with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb74_1.html Alpha-amylase]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOG OCA]. | | 1DOG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. The following page contains interesting information on the relation of 1DOG with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb74_1.html Alpha-amylase]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOG OCA]. |
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| ==Reference==
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| 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:[http://www.ncbi.nlm.nih.gov/pubmed/8431441 8431441]
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| [[Category: Alpha-amylase]] | | [[Category: Alpha-amylase]] |
| [[Category: Aspergillus awamori]] | | [[Category: Aspergillus awamori]] |
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| [[Category: Honzatko, R B.]] | | [[Category: Honzatko, R B.]] |
| [[Category: Hydrolase]] | | [[Category: Hydrolase]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:05:08 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 26 17:11:34 2008'' |
