1grf: Difference between revisions

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-[[Image:1grf.jpg|left|200px]]<br /><applet load="1grf" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1grf, resolution 2.0&Aring;" />
-'''SUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIVED FROM REFINED ENZYME: SUBSTRATE CRYSTAL STRUCTURES AT 2 ANGSTROMS RESOLUTION'''<br />
-==Overview==
+==SUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIVED FROM REFINED ENZYME: SUBSTRATE CRYSTAL STRUCTURES AT 2 ANGSTROMS RESOLUTION==
-The X-ray structure analyses of four glutathione reductase complexes and, derivatives have been extended to 2 A resolution and refined. The results, are discussed in conjunction with the structure of the oxidized native, enzyme known at 1.54 A resolution. While the residual co-ordinate errors, are around 0.2 A, some significant shifts even in this range could be, established. Points of particular interest are the 3.2 A approach of C4N, of nicotinamide to N5F of flavin in hydride transfer geometry, the, hydrogen bond geometries of the 2'-phosphate of NADPH as compared to, inferior geometries for an inorganic phosphate binding together with NADH, the differential mobilities of parts of the substrates as derived from, refined atomic temperature factors, and the stabilization of the thiolate, of the proximal Cys63 by conformational changes of neighboring residues as, well as by flavin. In addition, catalytically competent His467' is seen to, interact more optimally with the sulfur of glutathione-I than with the, distal sulfur of Cys58. The observed participation of water molecules for, both NADPH and glutathione binding is so extensive that a prediction of, the binding mode merely from the polypeptide structure would be very, difficult. The accurately known geometries allowed us to draw some, conclusions on the enzyme mechanism and suggest a possible scenario of the, catalysis.
+<StructureSection load='1grf' size='340' side='right'caption='[[1grf]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1grf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GRF 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACM:ACETAMIDE'>ACM</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1grf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1grf OCA], [https://pdbe.org/1grf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1grf RCSB], [https://www.ebi.ac.uk/pdbsum/1grf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1grf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GSHR_HUMAN GSHR_HUMAN] Maintains high levels of reduced glutathione in the cytosol.
+== 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/gr/1grf_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=1grf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray structure analyses of four glutathione reductase complexes and derivatives have been extended to 2 A resolution and refined. The results are discussed in conjunction with the structure of the oxidized native enzyme known at 1.54 A resolution. While the residual co-ordinate errors are around 0.2 A, some significant shifts even in this range could be established. Points of particular interest are the 3.2 A approach of C4N of nicotinamide to N5F of flavin in hydride transfer geometry, the hydrogen bond geometries of the 2'-phosphate of NADPH as compared to inferior geometries for an inorganic phosphate binding together with NADH, the differential mobilities of parts of the substrates as derived from refined atomic temperature factors, and the stabilization of the thiolate of the proximal Cys63 by conformational changes of neighboring residues as well as by flavin. In addition, catalytically competent His467' is seen to interact more optimally with the sulfur of glutathione-I than with the distal sulfur of Cys58. The observed participation of water molecules for both NADPH and glutathione binding is so extensive that a prediction of the binding mode merely from the polypeptide structure would be very difficult. The accurately known geometries allowed us to draw some conclusions on the enzyme mechanism and suggest a possible scenario of the catalysis.
-==Disease==
+Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution.,Karplus PA, Schulz GE J Mol Biol. 1989 Nov 5;210(1):163-80. PMID:2585516<ref>PMID:2585516</ref>
-Known diseases associated with this structure: Hemolytic anemia due to glutathione reductase deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=138300 138300]], Mental retardation, autosomal recessive, 6 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=138244 138244]]
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-GRF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=FAD:'>FAD</scene> and <scene name='pdbligand=ACM:'>ACM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutathione-disulfide_reductase Glutathione-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.7 1.8.1.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GRF OCA].
+</div>
+<div class="pdbe-citations 1grf" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution., Karplus PA, Schulz GE, J Mol Biol. 1989 Nov 5;210(1):163-80. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2585516 2585516]
+*[[Glutathione Reductase|Glutathione Reductase]]
-[[Category: Glutathione-disulfide reductase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Karplus, P.A.]]
+[[Category: Karplus PA]]
-[[Category: Schulz, G.E.]]
+[[Category: Schulz GE]]
-[[Category: ACM]]
-[[Category: FAD]]
-[[Category: PO4]]
-[[Category: oxidoreductase(flavoenzyme)]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:54:40 2008''