1dog: Difference between revisions
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[[Image:1dog.gif|left|200px]] | [[Image:1dog.gif|left|200px]] | ||
'''REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION''' | {{Structure | ||
|PDB= 1dog |SIZE=350|CAPTION= <scene name='initialview01'>1dog</scene>, resolution 2.3Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene> and <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</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] | |||
|GENE= | |||
}} | |||
'''REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1DOG is a [ | 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]. | ||
==Reference== | ==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:[http:// | 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] | ||
[[Category: Alpha-amylase]] | [[Category: Alpha-amylase]] | ||
[[Category: Aspergillus awamori]] | [[Category: Aspergillus awamori]] | ||
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[[Category: hydrolase]] | [[Category: hydrolase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:41:42 2008'' | ||
Revision as of 11:41, 20 March 2008
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| , resolution 2.3Å | |||||||
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| Ligands: | and | ||||||
| Activity: | Glucan 1,4-alpha-glucosidase, with EC number 3.2.1.3 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION
OverviewOverview
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 StructureAbout this Structure
1DOG is a Single protein structure of sequence from Aspergillus awamori. The following page contains interesting information on the relation of 1DOG with [Alpha-amylase]. Full crystallographic information is available from OCA.
ReferenceReference
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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