1st3: Difference between revisions

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-[[Image:1st3.jpg|left|200px]]<br /><applet load="1st3" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1st3, resolution 1.4&Aring;" />
-'''THE CRYSTAL STRUCTURE OF THE BACILLUS LENTUS ALKALINE PROTEASE, SUBTILISIN BL, AT 1.4 ANGSTROMS RESOLUTION'''<br />
-==Overview==
+==THE CRYSTAL STRUCTURE OF THE BACILLUS LENTUS ALKALINE PROTEASE, SUBTILISIN BL, AT 1.4 ANGSTROMS RESOLUTION==
-The crystal structure of subtilisin BL, an alkaline protease from Bacillus lentus with activity at pH 11, has been determined to 1.4 A resolution. The structure was solved by molecular replacement starting with the 2.1 A structure of subtilisin BPN' followed by molecular dynamics refinement using X-PLOR. A final crystallographic R-factor of 19% overall was obtained. The enzyme possesses stability at high pH, which is a result of the high pI of the protein. Almost all of the acidic side-chains are involved in some type of electrostatic interaction (ion pairs, calcium binding, etc.). Furthermore, three of seven tyrosine residues have potential partners for forming salt bridges. All of the potential partners are arginine with a pK around 12. Lysine would not function well in a salt bridge with tyrosine as it deprotonates at around the same pH as tyrosine ionizes. Stability at high pH is acquired in part from the pI of the protein, but also from the formation of salt bridges (which would affect the pI). The overall structure of the enzyme is very similar to other subtilisins and shows that the subtilisin fold is more highly conserved than would be expected from the differences in amino acid sequence. The amino acid side-chains in the hydrophobic core are not conserved, though the inter-residue interactions are. Finally, one third of the serine side-chains in the protein have multiple conformations. This presents an opportunity to correlate computer simulations with observed occupancies in the crystal structure.
+<StructureSection load='1st3' size='340' side='right'caption='[[1st3]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1st3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lederbergia_lenta Lederbergia lenta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ST3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ST3 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
+<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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1st3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1st3 OCA], [https://pdbe.org/1st3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1st3 RCSB], [https://www.ebi.ac.uk/pdbsum/1st3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1st3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUBB_LEDLE SUBB_LEDLE] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.
+== 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/st/1st3_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=1st3 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ST3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_lentus Bacillus lentus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ST3 OCA].
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution., Goddette DW, Paech C, Yang SS, Mielenz JR, Bystroff C, Wilke ME, Fletterick RJ, J Mol Biol. 1992 Nov 20;228(2):580-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1453465 1453465]
+[[Category: Large Structures]]
-[[Category: Bacillus lentus]]
+[[Category: Lederbergia lenta]]
-[[Category: Single protein]]
+[[Category: Goddette DW]]
-[[Category: Subtilisin]]
-[[Category: Goddette, D W.]]
-[[Category: CA]]
-[[Category: serine protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:04:56 2008''