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==Crystal structure of putative glucosidase lplD from bacillus subtilis==
==Crystal structure of putative glucosidase lplD from bacillus subtilis==
<StructureSection load='3fef' size='340' side='right' caption='[[3fef]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3fef' size='340' side='right'caption='[[3fef]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3fef]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FEF FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FEF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU07130, lplD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3fef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fef OCA], [https://pdbe.org/3fef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fef RCSB], [https://www.ebi.ac.uk/pdbsum/3fef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fef ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3fef TOPSAN]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Galacturan_1,4-alpha-galacturonidase Galacturan 1,4-alpha-galacturonidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.67 3.2.1.67] </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=3fef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fef OCA], [http://pdbe.org/3fef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fef RCSB], [http://www.ebi.ac.uk/pdbsum/3fef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fef ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/3fef TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/LPLD_BACSU LPLD_BACSU]] Alpha-galacturonidase able to catalyze the hydrolysis of the chromogenic substrate p-nitrophenyl-alpha-D-galacturonic acid (pNPalphaGalUA), and of the probable natural substrate alpha-1,4-di-galacturonate (GalUA(2)). Can neither hydrolyze pNPbetaGalUA, nor the stereoisomeric pNPalphaGlcUA. Does not display alpha- or beta-glucosidase activity as it fails to hydrolyze melibiose, raffinose, lactose and the chromogenic analogs, pNPalphaGal and pNPbetaGal. Can not use the following compounds as substrates: pNP-N-acetyl-alpha- and beta-D-galactosaminide, pNP-N-acetyl-alpha- and beta-D-glucosaminide, pNP-alpha-L- and beta-L-arabinopyranoside, pNP-alpha- and beta-D-glucuronide, pNP-alpha- and beta-D-glucopyranoside, pNP-alpha- and beta-D-glucopyranoside 6-phosphate, pNP-alpha-D-galactopyranoside 6-phosphate and oNP-beta-D-galactopyranoside 6-phosphate.<ref>PMID:23416295</ref> 
== 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/fe/3fef_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fe/3fef_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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=3fef 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=3fef ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Large Structures]]
[[Category: Galacturan 1,4-alpha-galacturonidase]]
[[Category: Almo SC]]
[[Category: Almo, S C]]
[[Category: Burley SK]]
[[Category: Burley, S K]]
[[Category: Rajashankar KR]]
[[Category: Structural genomic]]
[[Category: Ramagopal UA]]
[[Category: Rajashankar, K R]]
[[Category: Toro R]]
[[Category: Ramagopal, U A]]
[[Category: Toro, R]]
[[Category: Glycosidase]]
[[Category: Gulosidase]]
[[Category: Hydrolase]]
[[Category: Lpld]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Nad]]
[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
[[Category: PSI, Protein structure initiative]]
[[Category: Unknown function]]

Latest revision as of 01:48, 21 November 2024

Crystal structure of putative glucosidase lplD from bacillus subtilis

3fef, resolution 2.20Å

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