2jbf: Difference between revisions

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-[[Image:2jbf.jpg|left|200px]]
-<!--
+==Structure of PBP-A, L158E mutant. Acyl-enzyme complex with penicillin- G.==
-The line below this paragraph, containing "STRUCTURE_2jbf", creates the "Structure Box" on the page.
+<StructureSection load='2jbf' size='340' side='right'caption='[[2jbf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2jbf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pcc_6301 Pcc 6301]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JBF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PNM:OPEN+FORM+-+PENICILLIN+G'>PNM</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j7v|2j7v]], [[2j8y|2j8y]], [[2j9o|2j9o]]</div></td></tr>
-{{STRUCTURE_2jbf|  PDB=2jbf  |  SCENE=  }}
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></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=2jbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jbf OCA], [https://pdbe.org/2jbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jbf RCSB], [https://www.ebi.ac.uk/pdbsum/2jbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jbf ProSAT]</span></td></tr>
+</table>
+== 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/jb/2jbf_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=2jbf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Molecular evolution has always been a subject of discussions, and researchers are interested in understanding how proteins with similar scaffolds can catalyze different reactions. In the superfamily of serine penicillin-recognizing enzymes, D-alanyl-D-alanine peptidases and beta-lactamases are phylogenetically linked but feature large differences of reactivity towards their respective substrates. In particular, while beta-lactamases hydrolyze penicillins very fast, leading to their inactivation, these molecules inhibit d-alanyl-d-alanine peptidases by forming stable covalent penicilloyl enzymes. In cyanobacteria, we have discovered a new family of penicillin-binding proteins (PBPs) presenting all the sequence features of class A beta-lactamases but having a six-amino-acid deletion in the conserved Omega-loop and lacking the essential Glu166 known to be involved in the penicillin hydrolysis mechanism. With the aim of evolving a member of this family into a beta-lactamase, PBP-A from Thermosynechococcus elongatus has been chosen because of its thermostability. Based on sequence alignments, introduction of a glutamate in position 158 of the shorter Omega-loop afforded an enzyme with a 50-fold increase in the rate of penicillin hydrolysis. The crystal structures of PBP-A in the free and penicilloylated forms at 1.9 A resolution and of L158E mutant at 1.5 A resolution were also solved, giving insights in the catalytic mechanism of the proteins. Since all the active-site elements of PBP-A-L158E, including an essential water molecule, are almost perfectly superimposed with those of a class A beta-lactamase such as TEM-1, the question why our mutant is still 5 orders of magnitude less active as a penicillinase remains and our results emphasize how far we are from understanding the secrets of enzymes. Based on the few minor differences between the active sites of PBP-A and TEM-1, mutations were introduced in the L158E enzyme, but while activities on D-Ala-D-Ala mimicking substrates were severely impaired, further improvement in penicillinase activity was unsuccessful.
-'''STRUCTURE OF PBP-A, L158E MUTANT. ACYL-ENZYME COMPLEX WITH PENICILLIN-G.'''
+Structure of PBP-A from Thermosynechococcus elongatus, a penicillin-binding protein closely related to class A beta-lactamases.,Urbach C, Evrard C, Pudzaitis V, Fastrez J, Soumillion P, Declercq JP J Mol Biol. 2009 Feb 13;386(1):109-20. Epub 2008 Dec 9. PMID:19100272<ref>PMID:19100272</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jbf" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-JBF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus Synechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JBF OCA].
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pcc 6301]]
 [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-[[Category: Single protein]]
+[[Category: Declercq, J P]]
-[[Category: Synechococcus elongatus]]
+[[Category: Evrard, C]]
-[[Category: Declercq, J P.]]
-[[Category: Evrard, C.]]
 [[Category: Dd-peptidase]]
 [[Category: Hydrolase]]
@@ Line 24: / Line 45: @@
 [[Category: Penicillin-binding protein]]
 [[Category: Thioesterase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:38:41 2008''