1t6m

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(New page: 200px<br /><applet load="1t6m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1t6m, resolution 2.107&Aring;" /> '''X-ray Structure of ...)
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[[Image:1t6m.gif|left|200px]]<br /><applet load="1t6m" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1t6m, resolution 2.107&Aring;" />
 
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'''X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.'''<br />
 
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==Overview==
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==X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.==
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Phosphatidylinositol-specific phospholipase Cs (PLCs) are a family of, phosphodiesterases that catalyze the cleavage of the P-O bond via, transesterification using the internal hydroxyl group of the substrate as, a nucleophile, generating the five-membered cyclic inositol phosphate as, an intermediate or product. To better understand the role of calcium in, the catalytic mechanism of PLCs, we have determined the X-ray crystal, structure of an engineered PLC enzyme from Bacillus thuringiensis to 2.1 A, resolution. The active site of this enzyme has been altered by, substituting the catalytic arginine with an aspartate at position 69, (R69D). This single-amino acid substitution converted a metal-independent, low-molecular weight enzyme into a metal ion-dependent bacterial PLC with, an active site architecture similar to that of the larger metal, ion-dependent mammalian PLC. The Ca(2+) ion shows a distorted square, planar geometry in the active site that allows for efficient substrate, binding and transition state stabilization during catalysis. Additional, changes in the positions of the catalytic general acid/general base, (GA/GB) were also observed, indicating the interrelation of the intricate, hydrogen bonding network involved in stabilizing the active site amino, acids. The functional information provided by this X-ray structure now, allows for a better understanding of the catalytic mechanism, including, stereochemical effects and substrate interactions, which facilitates, better inhibitor design and sheds light on the possibilities of, understanding how protein evolution might have occurred across this enzyme, family.
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<StructureSection load='1t6m' size='340' side='right'caption='[[1t6m]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1t6m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6M 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]] 2.107&#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=1t6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6m OCA], [https://pdbe.org/1t6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6m RCSB], [https://www.ebi.ac.uk/pdbsum/1t6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6m ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PLC_BACTU PLC_BACTU] Cleaves glycosylphosphatidylinositol (GPI) and phosphatidylinositol (PI) anchors but not PI phosphates.
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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/t6/1t6m_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=1t6m ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1T6M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phosphatidylinositol_diacylglycerol-lyase Phosphatidylinositol diacylglycerol-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.13 4.6.1.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1T6M OCA].
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*[[Phospholipase C|Phospholipase C]]
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__TOC__
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==Reference==
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</StructureSection>
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X-ray structure of the R69D phosphatidylinositol-specific phospholipase C enzyme: insight into the role of calcium and surrounding amino acids in active site geometry and catalysis., Apiyo D, Zhao L, Tsai MD, Selby TL, Biochemistry. 2005 Aug 2;44(30):9980-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16042375 16042375]
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[[Category: Bacillus thuringiensis]]
[[Category: Bacillus thuringiensis]]
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[[Category: Phosphatidylinositol diacylglycerol-lyase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Apiyo D]]
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[[Category: Apiyo, D.]]
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[[Category: Selby TL]]
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[[Category: Selby, T.L.]]
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[[Category: Tsai M-D]]
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[[Category: Tsai, M.D.]]
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[[Category: Zhao L]]
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[[Category: Zhao, L.]]
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[[Category: CA]]
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[[Category: pi-plc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:01:38 2007''
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Current revision

X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.

PDB ID 1t6m

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