1ee6

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(New page: 200px<br /><applet load="1ee6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ee6, resolution 2.3&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
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[[Image:1ee6.gif|left|200px]]<br /><applet load="1ee6" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ee6, resolution 2.3&Aring;" />
 
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'''CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.==
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The crystal structure of a highly alkaline low molecular weight pectate, lyase (Pel-15) was determined at 1.5 A resolution by the multiple, isomorphous replacement (MIR) method. This is the first pectate lyase, structure from polysaccharide lyase family 3. The overall structure is a, simple eight-turn right-handed parallel beta-helix domain with one long, loop protruding from one side of the beta-helix. The low molecular weight, of Pel-15 derives from the lack of N- and C-terminal extensions that are, found in many beta-helix proteins. Although the structure has one calcium, ion at pH 6.7, raising the pH to 9.5 results in the binding of an, additional calcium ion. The common calcium ion found in both the pH 6.5, and 9.5 structures seems to stabilize both the beta-helix structure and, the long protruding loop. The additional calcium ion found in the pH 9.5, structure alone may neutralize the acidic substrate. The region around the, additional calcium ion is thought to bind to the substrate, as this region, is rich in charged amino-acid residues which are required in catalysis.
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<StructureSection load='1ee6' size='340' side='right'caption='[[1ee6]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ee6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._KSM-P15 Bacillus sp. KSM-P15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EE6 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]] 2.3&#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></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=1ee6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ee6 OCA], [https://pdbe.org/1ee6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ee6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ee6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ee6 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9RHW0_BACSP Q9RHW0_BACSP]
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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/ee/1ee6_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=1ee6 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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The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis.
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==About this Structure==
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The first structure of pectate lyase belonging to polysaccharide lyase family 3.,Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001, Nov 21. PMID:11717490<ref>PMID:11717490</ref>
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1EE6 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 CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EE6 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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The first structure of pectate lyase belonging to polysaccharide lyase family 3., Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T, Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001, Nov 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11717490 11717490]
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</div>
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[[Category: Bacillus sp.]]
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<div class="pdbe-citations 1ee6" style="background-color:#fffaf0;"></div>
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[[Category: Pectate lyase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Akita, M.]]
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__TOC__
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[[Category: Ito, S.]]
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</StructureSection>
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[[Category: Kobayashi, T.]]
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[[Category: Bacillus sp. KSM-P15]]
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[[Category: Suzuki, A.]]
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[[Category: Large Structures]]
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[[Category: Yamane, T.]]
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[[Category: Akita M]]
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[[Category: CA]]
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[[Category: Ito S]]
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[[Category: high-alkaline]]
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[[Category: Kobayashi T]]
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[[Category: low-molecular-weight]]
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[[Category: Suzuki A]]
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[[Category: parallel beta-helix]]
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[[Category: Yamane T]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:06:29 2007''
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Current revision

CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.

PDB ID 1ee6

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