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| - | [[Image:2e8z.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin== |
| - | |PDB= 2e8z |SIZE=350|CAPTION= <scene name='initialview01'>2e8z</scene>, resolution 2.20Å
| + | <StructureSection load='2e8z' size='340' side='right'caption='[[2e8z]], [[Resolution|resolution]] 2.20Å' scene=''> |
| - | |SITE= <scene name='pdbsite=AC1:Glc+Binding+Site+For+Residue+A+721'>AC1</scene>, <scene name='pdbsite=AC2:Glc+Binding+Site+For+Residue+A+722'>AC2</scene>, <scene name='pdbsite=AC3:Glc+Binding+Site+For+Residue+A+723'>AC3</scene>, <scene name='pdbsite=AC4:Glc+Binding+Site+For+Residue+A+724'>AC4</scene>, <scene name='pdbsite=AC5:Glc+Binding+Site+For+Residue+A+725'>AC5</scene>, <scene name='pdbsite=AC6:Glc+Binding+Site+For+Residue+A+726'>AC6</scene>, <scene name='pdbsite=AC7:Glc+Binding+Site+For+Residue+B+731'>AC7</scene>, <scene name='pdbsite=AC8:Glc+Binding+Site+For+Residue+B+732'>AC8</scene>, <scene name='pdbsite=AC9:Glc+Binding+Site+For+Residue+B+733'>AC9</scene>, <scene name='pdbsite=BC1:Glc+Binding+Site+For+Residue+B+734'>BC1</scene>, <scene name='pdbsite=BC2:Glc+Binding+Site+For+Residue+B+735'>BC2</scene>, <scene name='pdbsite=BC3:Glc+Binding+Site+For+Residue+B+736'>BC3</scene>, <scene name='pdbsite=BC4:Ca+Binding+Site+For+Residue+A+741'>BC4</scene>, <scene name='pdbsite=BC5:Ca+Binding+Site+For+Residue+B+742'>BC5</scene>, <scene name='pdbsite=BC6:Act+Binding+Site+For+Residue+A+751'>BC6</scene>, <scene name='pdbsite=BC7:Act+Binding+Site+For+Residue+B+752'>BC7</scene>, <scene name='pdbsite=BC8:Gol+Binding+Site+For+Residue+A+761'>BC8</scene> and <scene name='pdbsite=BC9:Gol+Binding+Site+For+Residue+B+762'>BC9</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
| + | <table><tr><td colspan='2'>[[2e8z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E8Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E8Z FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pullulanase Pullulanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.41 3.2.1.41] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | |GENE= amyX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900015:alpha-cyclodextrin'>PRD_900015</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e8z OCA], [https://pdbe.org/2e8z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e8z RCSB], [https://www.ebi.ac.uk/pdbsum/2e8z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e8z ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[2e8y|2E8Y]], [[2e9b|2E9B]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e8z OCA], [http://www.ebi.ac.uk/pdbsum/2e8z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e8z RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/PULA_BACSU PULA_BACSU] |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/2e8z_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </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=2e8z ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin'''
| + | ==See Also== |
| - | | + | *[[Amylase 3D structures|Amylase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | The AmyX gene encoding pullulanase from the common spore-forming bacterium Bacillus subtilis strain 168 was cloned, overexpressed in Escherichia coli, purified and crystallized. The recombinant pullulanase was purified to homogeneity using ammonium sulfate precipitation, hydrophobic chromatography and anion-exchange chromatography, resulting in a specific activity of 24.10 U per milligram of protein. SDS-PAGE analysis showed that the molecular weight of the protein is approximately 81.0 kDa, which is similar to the calculated molecular weight, 81.1 kDa, from its translated cDNA sequence. The k(cat) and K(m) of the purified enzyme with pullulan as substrate were approximately 79 s(-1) and 1.284 mg ml(-1), respectively. X-ray crystallographic analysis of the pullulanase crystal showed that the crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 70.568, b = 127.68, c = 189.25 angstroms. The crystal contains two molecules of pullulanase in the asymmetric unit, with a solvent content of 53.15%. The crystal diffracted to 2.1 angstroms resolution at a synchrotron and is suitable for structure determination.
| + | |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2E8Z is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E8Z OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168., Malle D, Itoh T, Hashimoto W, Murata K, Utsumi S, Mikami B, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt, 4):381-4. Epub 2006 Mar 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16582490 16582490]
| + | |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| - | [[Category: Pullulanase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Iwamoto H]] |
| - | [[Category: Iwamoto, H.]] | + | [[Category: Katsuya Y]] |
| - | [[Category: Katsuya, Y.]] | + | [[Category: Malle D]] |
| - | [[Category: Malle, D.]] | + | [[Category: Mikami B]] |
| - | [[Category: Mikami, B.]] | + | [[Category: Utsumi S]] |
| - | [[Category: Utsumi, S.]] | + | |
| - | [[Category: alpha-amylase-family]]
| + | |
| - | [[Category: alpha-cyclodextrin]]
| + | |
| - | [[Category: beta-alpha-barrel]]
| + | |
| - | [[Category: hydrolase]]
| + | |
| - | [[Category: multiple domain]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:45:34 2008''
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