2jfq: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2jfq.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2jfq", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2jfq|  PDB=2jfq  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE'''
+==Crystal structure of Staphylococcus aureus glutamate racemase in complex with D- Glutamate==
+<StructureSection load='2jfq' size='340' side='right'caption='[[2jfq]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2jfq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFQ 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]] 2.15&#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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jfq OCA], [https://pdbe.org/2jfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jfq RCSB], [https://www.ebi.ac.uk/pdbsum/2jfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jfq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MURI_STAAR MURI_STAAR] Provides the (R)-glutamate required for cell wall biosynthesis.[HAMAP-Rule:MF_00258]
+== 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/2jfq_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=2jfq 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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-JFQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JFQ OCA].
+</div>
+<div class="pdbe-citations 2jfq" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Glutamate racemase 3D structures|Glutamate racemase 3D structures]]
-[[Category: Glutamate racemase]]
+== References ==
-[[Category: Single protein]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Staphylococcus aureus]]
-[[Category: Lundqvist, T.]]
+[[Category: Lundqvist T]]
-[[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 Sun May  4 08:50:45 2008''