2gvy

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[[Image:2gvy.gif|left|200px]]
 
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{{Structure
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==Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution==
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|PDB= 2gvy |SIZE=350|CAPTION= <scene name='initialview01'>2gvy</scene>, resolution 1.800&Aring;
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<StructureSection load='2gvy' size='340' side='right'caption='[[2gvy]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene> and <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
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<table><tr><td colspan='2'>[[2gvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GVY FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1]
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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]] 1.8&#8491;</td></tr>
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|GENE= amy1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5062 Aspergillus oryzae])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=PRD_900018:beta-maltose'>PRD_900018</scene></td></tr>
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}}
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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=2gvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gvy OCA], [https://pdbe.org/2gvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gvy RCSB], [https://www.ebi.ac.uk/pdbsum/2gvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gvy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AMYA1_ASPOR AMYA1_ASPOR]
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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/gv/2gvy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2gvy ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P2(1)2(1)2(1) with one molecule per asymmetric unit and one belongs to the monoclinic space group P2(1) with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger alpha-amylase crystallized in the monoclinic space group P2(1) with two molecules per asymmetric unit in complex with maltose at 1.8 angstroms resolution is reported. Furthermore, a novel 1.6 angstroms resolution orthorhombic crystal form (space group P2(1)2(1)2) of the native enzyme is presented. Four maltose molecules are observed in the maltose-alpha-amylase complex. Three of these occupy active-site subsites -2 and -1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.
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'''Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution'''
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Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.,Vujicic-Zagar A, Dijkstra BW Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt, 8):716-21. Epub 2006 Jul 24. PMID:16880540<ref>PMID:16880540</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2gvy" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P2(1)2(1)2(1) with one molecule per asymmetric unit and one belongs to the monoclinic space group P2(1) with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger alpha-amylase crystallized in the monoclinic space group P2(1) with two molecules per asymmetric unit in complex with maltose at 1.8 angstroms resolution is reported. Furthermore, a novel 1.6 angstroms resolution orthorhombic crystal form (space group P2(1)2(1)2) of the native enzyme is presented. Four maltose molecules are observed in the maltose-alpha-amylase complex. Three of these occupy active-site subsites -2 and -1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.
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*[[Amylase 3D structures|Amylase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2GVY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GVY OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution., Vujicic-Zagar A, Dijkstra BW, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt, 8):716-21. Epub 2006 Jul 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16880540 16880540]
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[[Category: Alpha-amylase]]
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[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dijkstra, B W.]]
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[[Category: Dijkstra BW]]
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[[Category: Vujicic-Zagar, A.]]
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[[Category: Vujicic-Zagar A]]
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[[Category: CA]]
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[[Category: NAG]]
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[[Category: (beta-alpha)8 barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:09:49 2008''
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Current revision

Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution

PDB ID 2gvy

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