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1dog

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[[Image:1dog.gif|left|200px]]
 
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==REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION==
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The line below this paragraph, containing "STRUCTURE_1dog", creates the "Structure Box" on the page.
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<StructureSection load='1dog' size='340' side='right'caption='[[1dog]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dog]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. The February 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DOG FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</scene></td></tr>
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{{STRUCTURE_1dog| PDB=1dog | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dog OCA], [https://pdbe.org/1dog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dog RCSB], [https://www.ebi.ac.uk/pdbsum/1dog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dog ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AMYG_ASPAW AMYG_ASPAW]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/do/1dog_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dog ConSurf].
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<div style="clear:both"></div>
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'''REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION'''
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==See Also==
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*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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., &amp; 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==
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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: Glucan 1,4-alpha-glucosidase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Aleshin, A.]]
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[[Category: Aleshin A]]
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[[Category: Firsov, L.]]
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[[Category: Firsov L]]
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[[Category: Harris, E.]]
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[[Category: Harris E]]
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[[Category: Honzatko, R B.]]
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[[Category: Honzatko RB]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:05:08 2008''
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Current revision

REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION

PDB ID 1dog

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