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==Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin==
==Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin==
<StructureSection load='2e8z' size='340' side='right' caption='[[2e8z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2e8z' size='340' side='right'caption='[[2e8z]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2e8z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E8Z FirstGlance]. <br>
<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>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e8y|2e8y]], [[2e9b|2e9b]]</td></tr>
<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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amyX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
<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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/2e8z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e8z RCSB], [http://www.ebi.ac.uk/pdbsum/2e8z PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PULA_BACSU PULA_BACSU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e8/2e8z_consurf.spt"</scriptWhenChecked>
     <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>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 20:
</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16582490<ref>PMID:16582490</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2e8z" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Amylase|Amylase]]
*[[Amylase 3D structures|Amylase 3D structures]]
*[[User:Gabriel Pons/Sandbox 2|User:Gabriel Pons/Sandbox 2]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus globigii migula 1900]]
[[Category: Bacillus subtilis]]
[[Category: Pullulanase]]
[[Category: Large Structures]]
[[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]]

Latest revision as of 11:37, 25 October 2023

Crystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrinCrystal structure of pullulanase type I from Bacillus subtilis str. 168 complexed with alpha-cyclodextrin

Structural highlights

2e8z is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PULA_BACSU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2e8z, resolution 2.20Å

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