6gsu: Difference between revisions

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-{{Seed}}
-[[Image:6gsu.png|left|200px]]
-<!--
+==FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIVE SITE OF A CLASS MU GLUTATHIONE TRANSFERASE==
-The line below this paragraph, containing "STRUCTURE_6gsu", creates the "Structure Box" on the page.
+<StructureSection load='6gsu' size='340' side='right'caption='[[6gsu]], [[Resolution|resolution]] 1.85&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'>[[6gsu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_rattus Rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GSU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GSU 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPS:L-GAMMA-GLUTAMYL-S-[(9S,10S)-10-HYDROXY-9,10-DIHYDROPHENANTHREN-9-YL]-L-CYSTEINYLGLYCINE'>GPS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_6gsu|  PDB=6gsu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6gsu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gsu OCA], [https://pdbe.org/6gsu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gsu RCSB], [https://www.ebi.ac.uk/pdbsum/6gsu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gsu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GSTM1_RAT GSTM1_RAT] Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. The olfactory GST may be crucial for the acuity of the olfactory process.
+== 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/gs/6gsu_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=6gsu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The activation of the thiol of glutathione (GSH) bound in the active site of the class mu glutathione transferase M1-1 from rat involves a hydrogen-bonding network that includes a direct (first-sphere) interaction between the hydroxyl group of Y6 and the sulfur of GSH and second-sphere interactions involving a hydrogen bond between the main-chain amide N-H of L12 and the hydroxyl group of Y6 and an on-face hydrogen bond between the hydroxyl group of T13 and the pi-electron cloud of Y6 (i.e., T13-OH---pi-Y6-OH--- -SG). The functions of these hydrogen bonds have been examined with a combination of site-specific mutagenesis and X-ray crystallography. The hydroxyl group of Y6 has a normal pKa of about 10 even though it is shielded from solvent and is in a largely hydrophobic environment. The apparent pKa of GSH in the binary Y6F.GSH complex is increased by 1.6 log units, and the reactivity of the enzyme-bound nucleophile is reduced. The catalytic properties of the Y6L mutant are identical to those of Y6F, suggesting that the weakly polar on-edge interaction between the aromatic ring and sulfur has no influence on catalysis. The refined three-dimensional structure of the Y6F mutant in complex with GSH shows no major structural perturbation of the protein other than a change in the coordination environment of the sulfur. Removal of the second-sphere influence of the on-face hydrogen bond between the hydroxyl groups T13 as in the T13V and T13A mutants elevates the pKa of enzyme-bound GSH by about 0.7 pKa units. Crystal structures of these mutants show that structural changes in the active site are minor and suggest that the changes in pKa of E.GSH are due to the presence or absence of the on-face hydrogen bond. The T13S mutant has a completely different side-chain hydrogen-bonding geometry than T13 in the native enzyme and catalytic properties similar to the T13A and T13V mutants consistent with the absence of an on-face hydrogen bond. The gamma-methyl group of T13 is essential in enforcing the on-face hydrogen bond geometry and preventing the hydroxyl group from forming more favorable conventional hydrogen bonds.
-===FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIVE SITE OF A CLASS MU GLUTATHIONE TRANSFERASE===
+First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase.,Xiao G, Liu S, Ji X, Johnson WW, Chen J, Parsons JF, Stevens WJ, Gilliland GL, Armstrong RN Biochemistry. 1996 Apr 16;35(15):4753-65. PMID:8664265<ref>PMID:8664265</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6gsu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8664265}}, adds the Publication Abstract to the page
+*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8664265 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8664265}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-GSU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_rattus Rattus rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GSU OCA].
-==Reference==
-First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase., Xiao G, Liu S, Ji X, Johnson WW, Chen J, Parsons JF, Stevens WJ, Gilliland GL, Armstrong RN, Biochemistry. 1996 Apr 16;35(15):4753-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8664265 8664265]
-[[Category: Glutathione transferase]]
 [[Category: Rattus rattus]]
-[[Category: Single protein]]
+[[Category: Armstrong RN]]
-[[Category: Armstrong, R N.]]
+[[Category: Gilliland GL]]
-[[Category: Gilliland, G L.]]
+[[Category: Ji X]]
-[[Category: Ji, X.]]
+[[Category: Xiao G]]
-[[Category: Xiao, G.]]
-[[Category: Glutathione transferase]]
-[[Category: Isoenzyme 3-3]]
-[[Category: T13a mutant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 14:19:48 2008''