2jfx: Difference between revisions

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-[[Image:2jfx.jpg|left|200px]]
- {{Structure
+==Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate==
-|PDB= 2jfx |SIZE=350|CAPTION= <scene name='initialview01'>2jfx</scene>, resolution 2.3&Aring;
+<StructureSection load='2jfx' size='340' side='right'caption='[[2jfx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Dgl+Binding+Site+For+Chain+B'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DGL:D-GLUTAMIC ACID'>DGL</scene>
+<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>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Glutamate_racemase Glutamate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.3 5.1.1.3]
+</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>
-|GENE=
+<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>
-}}
+<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>
-==Overview==
+==See Also==
-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.
+*[[Glutamate racemase 3D structures|Glutamate racemase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-JFX is a [[Single protein]] structure of sequence 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].
+__TOC__
+</StructureSection>
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17568739 17568739]
-[[Category: Glutamate racemase]]
 [[Category: Helicobacter pylori]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Lundqvist, T.]]
+[[Category: Lundqvist T]]
-[[Category: Xue, Y.]]
+[[Category: Xue Y]]
-[[Category: DGL]]
-[[Category: cell shape]]
-[[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 Thu Mar 20 17:41:24 2008''