2ime: Difference between revisions

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 ==2-Hydroxychromene-2-carboxylate Isomerase: a Kappa Class Glutathione-S-Transferase from Pseudomonas putida==
-<StructureSection load='2ime' size='340' side='right' caption='[[2ime]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='2ime' size='340' side='right'caption='[[2ime]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ime]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IME FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ime]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IME FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2C2:(2S)-2-HYDROXY-2H-CHROMENE-2-CARBOXYLIC+ACID'>2C2</scene>, <scene name='pdbligand=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOH:(3E)-4-(2-HYDROXYPHENYL)-2-OXOBUT-3-ENOIC+ACID'>TOH</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r4w|1r4w]], [[2imd|2imd]], [[2imf|2imf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2C2:(2S)-2-HYDROXY-2H-CHROMENE-2-CARBOXYLIC+ACID'>2C2</scene>, <scene name='pdbligand=CXS:3-CYCLOHEXYL-1-PROPYLSULFONIC+ACID'>CXS</scene>, <scene name='pdbligand=GSH:GLUTATHIONE'>GSH</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOH:(3E)-4-(2-HYDROXYPHENYL)-2-OXOBUT-3-ENOIC+ACID'>TOH</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nahD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</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=2ime FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ime OCA], [https://pdbe.org/2ime PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ime RCSB], [https://www.ebi.ac.uk/pdbsum/2ime PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ime ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutathione_transferase Glutathione transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.18 2.5.1.18] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ime FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ime OCA], [http://pdbe.org/2ime PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ime RCSB], [http://www.ebi.ac.uk/pdbsum/2ime PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAHD_PSEPU NAHD_PSEPU]] Involved in the naphthalene catabolic pathway. Catalyzes the reversible glutathione-dependent isomerization of 2-hydroxychromene-2-carboxylate (HCCA) to trans-O-hydroxybenzylidenepyruvate (THBPA).<ref>PMID:8002605</ref> <ref>PMID:1447127</ref>
+[https://www.uniprot.org/uniprot/NAHD_PSEPU NAHD_PSEPU] Involved in the naphthalene catabolic pathway. Catalyzes the reversible glutathione-dependent isomerization of 2-hydroxychromene-2-carboxylate (HCCA) to trans-O-hydroxybenzylidenepyruvate (THBPA).<ref>PMID:8002605</ref> <ref>PMID:1447127</ref>
 == 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/im/2ime_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2ime_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ime ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The enzyme 2-hydroxychromene-2-carboxylic acid (HCCA) isomerase catalyzes the glutathione (GSH)-dependent interconversion (Keq = 1.5) of HCCA and trans-o-hydroxybenzylidene pyruvic acid (tHBPA) in the naphthalene catabolic pathway of Pseudomonas putida. The dimeric protein binds one molecule of GSH very tightly (Kd approximately 5 nM) and a second molecule of GSH with much lower affinity (Kd approximately 2 to 11 microM). The enzyme is unstable in the absence of GSH. The turnover number in the forward direction (47 s(-1) at 25 degrees C) greatly exceeds off rates for GSH (koff approximately 10(-3) to 10(-2) s(-1) at 10 degrees C), suggesting that GSH acts as a tightly bound cofactor in the reaction. The crystal structure of the enzyme at 1.7 A resolution reveals that the isomerase is closely related to class kappa GSH transferases. Diffraction quality crystals could only be obtained in the presence of GSH and HCCA/tHBPA. Clear electron density is seen for GSH. Electron density for the organic substrates is located near the GSH and is best modeled to include both HCCA and tHBPA at occupancies of 0.5 for each. Although there is no electron density connecting the sulfur of GSH to the organic substrates, the sulfur is located very close (2.78 A) to C7 of HCCA. Taken together, the results suggest that the isomerization reaction involves a short-lived covalent adduct between the sulfur of GSH and C7 of the substrate.
--Hydroxychromene-2-carboxylic acid isomerase: a kappa class glutathione transferase from Pseudomonas putida.,Thompson LC, Ladner JE, Codreanu SG, Harp J, Gilliland GL, Armstrong RN Biochemistry. 2007 Jun 12;46(23):6710-22. Epub 2007 May 18. PMID:17508726<ref>PMID:17508726</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
-<div class="pdbe-citations 2ime" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus fluorescens putidus flugge 1886]]
+[[Category: Large Structures]]
-[[Category: Glutathione transferase]]
+[[Category: Pseudomonas putida]]
-[[Category: Armstrong, R N]]
+[[Category: Armstrong RN]]
-[[Category: Codreanu, S G]]
+[[Category: Codreanu SG]]
-[[Category: Gilliland, G L]]
+[[Category: Gilliland GL]]
-[[Category: Harp, J]]
+[[Category: Harp J]]
-[[Category: Ladner, J E]]
+[[Category: Ladner JE]]
-[[Category: Thompson, L C]]
+[[Category: Thompson LC]]
-[[Category: Glutathione]]
-[[Category: Isomerase]]
-[[Category: Kappa gst]]
-[[Category: Kgst]]
-[[Category: Transferase]]