2jfx: Difference between revisions

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-{{Seed}}
-[[Image:2jfx.png|left|200px]]
-<!--
+==Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate==
-The line below this paragraph, containing "STRUCTURE_2jfx", creates the "Structure Box" on the page.
+<StructureSection load='2jfx' size='340' side='right'caption='[[2jfx]], [[Resolution|resolution]] 2.30&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'>[[2jfx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFX FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=DGL:D-GLUTAMIC+ACID'>DGL</scene></td></tr>
-{{STRUCTURE_2jfx|  PDB=2jfx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfx OCA], [https://pdbe.org/2jfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfx RCSB], [https://www.ebi.ac.uk/pdbsum/2jfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MURI_HELPJ MURI_HELPJ] Provides the (R)-glutamate required for cell wall biosynthesis (By similarity).
+== 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/jf/2jfx_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=2jfx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.
-===CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE===
+Exploitation of structural and regulatory diversity in glutamate racemases.,Lundqvist T, Fisher SL, Kern G, Folmer RH, Xue Y, Newton DT, Keating TA, Alm RA, de Jonge BL Nature. 2007 Jun 14;447(7146):817-22. PMID:17568739<ref>PMID:17568739</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jfx" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17568739}}, adds the Publication Abstract to the page
+*[[Glutamate racemase 3D structures|Glutamate racemase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17568739 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17568739}}
+__TOC__
+</StructureSection>
-==About this Structure==
-JFX is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFX OCA].
-==Reference==
-<ref group="xtra">PMID:17568739</ref><references group="xtra"/>
-[[Category: Glutamate racemase]]
 [[Category: Helicobacter pylori]]
-[[Category: Lundqvist, T.]]
+[[Category: Large Structures]]
-[[Category: Xue, Y.]]
+[[Category: Lundqvist T]]
-[[Category: Cell shape]]
+[[Category: Xue Y]]
-[[Category: Cell wall]]
-[[Category: Glutamate racemase]]
-[[Category: Isomerase]]
-[[Category: Peptidoglycan biosynthesis]]
-[[Category: Peptidoglycan synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:02:05 2009''