1yb4: Difference between revisions

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-[[Image:1yb4.gif|left|200px]]
-<!--
+==Crystal Structure of the Tartronic Semialdehyde Reductase from Salmonella typhimurium LT2==
-The line below this paragraph, containing "STRUCTURE_1yb4", creates the "Structure Box" on the page.
+<StructureSection load='1yb4' size='340' side='right'caption='[[1yb4]], [[Resolution|resolution]] 2.40&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'>[[1yb4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YB4 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1yb4|  PDB=1yb4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yb4 OCA], [https://pdbe.org/1yb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yb4 RCSB], [https://www.ebi.ac.uk/pdbsum/1yb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yb4 ProSAT], [https://www.topsan.org/Proteins/MCSG/1yb4 TOPSAN]</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/yb/1yb4_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=1yb4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tartronate semialdehyde reductases (TSRs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using NAD as cofactor in the final stage of D: -glycerate biosynthesis. These enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. Here, we present the crystal structure of GarR a TSR from Salmonella typhimurium determined by the single-wavelength anomalous diffraction method and refined to 1.65 A resolution. The active site of the enzyme contains L: -tartrate which most likely mimics a position of a glycerate which is a product of the enzyme reaction. The analysis of the TSR structure shows also a putative NADPH binding site in the enzyme.
-'''Crystal Structure of the Tartronic Semialdehyde Reductase from Salmonella typhimurium LT2'''
+X-Ray crystal structure of GarR-tartronate semialdehyde reductase from Salmonella typhimurium.,Osipiuk J, Zhou M, Moy S, Collart F, Joachimiak A J Struct Funct Genomics. 2009 Jan 28. PMID:19184529<ref>PMID:19184529</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-YB4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium_lt2 Salmonella typhimurium lt2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YB4 OCA].
+<div class="pdbe-citations 1yb4" style="background-color:#fffaf0;"></div>
-[[Category: 2-hydroxy-3-oxopropionate reductase]]
+== References ==
-[[Category: Salmonella typhimurium lt2]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Collart, F.]]
+</StructureSection>
-[[Category: Joachimiak, A.]]
+[[Category: Large Structures]]
-[[Category: Kim, Y.]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Collart F]]
-[[Category: Wu, R.]]
+[[Category: Joachimiak A]]
-[[Category: Mcsg]]
+[[Category: Kim Y]]
-[[Category: Oxidoreductase]]
+[[Category: Wu R]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Salmonella typhimurium lt2]]
-[[Category: Structural genomic]]
-[[Category: Tartronic semialdehyde reductase]]
-[[Category: The midwest center for structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 16:06:01 2008''