1gbi: Difference between revisions

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-[[Image:1gbi.jpg|left|200px]]<br /><applet load="1gbi" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1gbi, resolution 2.30&Aring;" />
-'''ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID'''<br />
-==Overview==
+==ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA AND GLY 216 REPLACED BY LEU COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-PHENYLALANINE BORONIC ACID==
-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.
+<StructureSection load='1gbi' size='340' side='right'caption='[[1gbi]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GBI 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]] 2.3&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gbi OCA], [https://pdbe.org/1gbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gbi RCSB], [https://www.ebi.ac.uk/pdbsum/1gbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gbi ProSAT]</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/1gbi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1gbi 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.
-==About this Structure==
+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>
-GBI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GBI OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7500345 7500345]
+</div>
-[[Category: Alpha-lytic endopeptidase]]
+<div class="pdbe-citations 1gbi" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Alpha-lytic protease 3D structures|Alpha-lytic protease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Lysobacter enzymogenes]]
-[[Category: Single protein]]
+[[Category: Agard DA]]
-[[Category: Agard, D.A.]]
+[[Category: Mace JE]]
-[[Category: Mace, J.E.]]
-[[Category: SO4]]
-[[Category: active-site mutation]]
-[[Category: inhibitor complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:54:25 2007''