1gbm: Difference between revisions

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 ==ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID==
-<StructureSection load='1gbm' size='340' side='right' caption='[[1gbm]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
+<StructureSection load='1gbm' size='340' side='right'caption='[[1gbm]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gbm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29487 Atcc 29487]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p08 1p08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GBM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gbm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1p08 1p08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GBM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.28&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=B2F:PHENYLALANINE+BORONIC+ACID'>B2F</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B2F:PHENYLALANINE+BORONIC+ACID'>B2F</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</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">ALPHA-LYTIC PROTEASE PREPROENZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69 ATCC 29487])</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=1gbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gbm OCA], [https://pdbe.org/1gbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gbm RCSB], [https://www.ebi.ac.uk/pdbsum/1gbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gbm 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/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </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=1gbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gbm RCSB], [http://www.ebi.ac.uk/pdbsum/1gbm PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRLA_LYSEN PRLA_LYSEN]
 == 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/gb/1gbm_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gb/1gbm_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/chain_selection.php?pdb_ID=2ata 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=1gbm ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without abolishing catalysis, and have major effects upon the substrate specificity of the enzyme. Kinetic characterization of eleven enzymatically active mutants against a panel of eight substrates clearly revealed the functional consequences of the substitutions at position 216. To understand better the structural basis for their altered specificity, the GA216 + MA190 and GL216 + MA190 mutants have been crystallized both with and without a representative series of peptide boronic acid transition-state analog inhibitors. An empirical description and non-parametric statistical analysis of structural variation among these enzyme: inhibitor complexes is presented. The roles of active site plasticity and dynamics in alpha-lytic protease function and substrate preference are also addressed. The results strongly suggest that substrate specificity determination in alpha-lytic protease is a distributed property of the active site and substrate molecule.
-Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity.,Mace JE, Agard DA J Mol Biol. 1995 Dec 8;254(4):720-36. PMID:7500345<ref>PMID:7500345</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Alpha-lytic protease|Alpha-lytic protease]]
+*[[Alpha-lytic protease 3D structures|Alpha-lytic protease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Alpha-lytic endopeptidase]]
+[[Category: Large Structures]]
-[[Category: Atcc 29487]]
+[[Category: Lysobacter enzymogenes]]
-[[Category: Agard, D A]]
+[[Category: Agard DA]]
-[[Category: Mace, J E]]
+[[Category: Mace JE]]
-[[Category: Active-site mutation]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Serine proteinase]]