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2d3n

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(New page: 200px<br /><applet load="2d3n" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d3n, resolution 1.90&Aring;" /> '''Crystal structure of...)
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[[Image:2d3n.gif|left|200px]]<br /><applet load="2d3n" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d3n, resolution 1.90&Aring;" />
 
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'''Crystal structure of maltohexaose-producing amylase from Bacillus sp.707 complexed with maltohexaose'''<br />
 
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==Overview==
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==Crystal structure of maltohexaose-producing amylase from Bacillus sp.707 complexed with maltohexaose==
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Maltohexaose-producing amylase (G6-amylase) from alkalophilic Bacillus, sp.707 predominantly produces maltohexaose (G6) in the yield of &gt;30% of, the total products from short-chain amylose (DP=17). Our previous, crystallographic study showed that G6-amylase has nine subsites, from -6, to +3, and pointed out the importance of the indole moiety of Trp140 in G6, production. G6-amylase has very low levels of hydrolytic activities for, oligosaccharides shorter than maltoheptaose. To elucidate the mechanism, underlying G6 production, we determined the crystal structures of the, G6-amylase complexes with G6 and maltopentaose (G5). In the active site of, the G6-amylase/G5 complex, G5 is bound to subsites -6 to -2, while G1 and, G6 are found at subsites +2 and -7 to -2, respectively, in the, G6-amylase/G6 complex. In both structures, the glucosyl residue located at, subsite -6 is stacked to the indole moiety of Trp140 within a distance of, 4A. The measurement of the activities of the mutant enzymes when Trp140, was replaced by leucine (W140L) or by tyrosine (W140Y) showed that the G6, production from short-chain amylose by W140L is lower than that by W140Y, or wild-type enzyme. The face-to-face short contact between Trp140 and, substrate sugars is suggested to regulate the disposition of the glucosyl, residue at subsite -6 and to govern product specificity for G6 production.
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<StructureSection load='2d3n' size='340' side='right'caption='[[2d3n]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d3n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._707 Bacillus sp. 707]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3N 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]] 1.9&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=PRD_900009:alpha-maltotriose'>PRD_900009</scene>, <scene name='pdbligand=PRD_900010:alpha-maltotetraose'>PRD_900010</scene>, <scene name='pdbligand=PRD_900035:alpha-maltohexaose'>PRD_900035</scene></td></tr>
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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=2d3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3n OCA], [https://pdbe.org/2d3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3n RCSB], [https://www.ebi.ac.uk/pdbsum/2d3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3n ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AMT6_BACS7 AMT6_BACS7]
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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/d3/2d3n_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=2d3n 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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Maltohexaose-producing amylase (G6-amylase) from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) in the yield of &gt;30% of the total products from short-chain amylose (DP=17). Our previous crystallographic study showed that G6-amylase has nine subsites, from -6 to +3, and pointed out the importance of the indole moiety of Trp140 in G6 production. G6-amylase has very low levels of hydrolytic activities for oligosaccharides shorter than maltoheptaose. To elucidate the mechanism underlying G6 production, we determined the crystal structures of the G6-amylase complexes with G6 and maltopentaose (G5). In the active site of the G6-amylase/G5 complex, G5 is bound to subsites -6 to -2, while G1 and G6 are found at subsites +2 and -7 to -2, respectively, in the G6-amylase/G6 complex. In both structures, the glucosyl residue located at subsite -6 is stacked to the indole moiety of Trp140 within a distance of 4A. The measurement of the activities of the mutant enzymes when Trp140 was replaced by leucine (W140L) or by tyrosine (W140Y) showed that the G6 production from short-chain amylose by W140L is lower than that by W140Y or wild-type enzyme. The face-to-face short contact between Trp140 and substrate sugars is suggested to regulate the disposition of the glucosyl residue at subsite -6 and to govern product specificity for G6 production.
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==About this Structure==
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Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707.,Kanai R, Haga K, Akiba T, Yamane K, Harata K Protein Sci. 2006 Mar;15(3):468-77. Epub 2006 Feb 1. PMID:16452622<ref>PMID:16452622</ref>
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2D3N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.] with GLC, CA and NA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glucan_1,4-alpha-maltohexaosidase Glucan 1,4-alpha-maltohexaosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.98 3.2.1.98] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D3N OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Role of Trp140 at subsite -6 on the maltohexaose production of maltohexaose-producing amylase from alkalophilic Bacillus sp.707., Kanai R, Haga K, Akiba T, Yamane K, Harata K, Protein Sci. 2006 Mar;15(3):468-77. Epub 2006 Feb 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16452622 16452622]
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</div>
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[[Category: Bacillus sp.]]
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<div class="pdbe-citations 2d3n" style="background-color:#fffaf0;"></div>
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[[Category: Glucan 1,4-alpha-maltohexaosidase]]
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[[Category: Single protein]]
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[[Category: Akiba, T.]]
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[[Category: Haga, K.]]
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[[Category: Harata, K.]]
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[[Category: Kanai, R.]]
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[[Category: Yamane, K.]]
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[[Category: CA]]
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[[Category: GLC]]
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[[Category: NA]]
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[[Category: ligand binding]]
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[[Category: maltohexaose]]
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[[Category: protein-carbohydrate complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:25:26 2007''
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==See Also==
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*[[Amylase 3D structures|Amylase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus sp. 707]]
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[[Category: Large Structures]]
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[[Category: Akiba T]]
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[[Category: Haga K]]
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[[Category: Harata K]]
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[[Category: Kanai R]]
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[[Category: Yamane K]]

Current revision

Crystal structure of maltohexaose-producing amylase from Bacillus sp.707 complexed with maltohexaose

PDB ID 2d3n

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