3ypi: Difference between revisions

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-[[Image:3ypi.jpg|left|200px]]<br /><applet load="3ypi" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="3ypi, resolution 2.8&Aring;" />
-'''ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF HISTIDINE-95'''<br />
-==Overview==
+==ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF HISTIDINE-95==
-Electrophilic catalysis by histidine-95 in triosephosphate isomerase has, been probed by using Fourier transform infrared spectroscopy and X-ray, crystallography. The carbonyl stretching frequency of dihydroxyacetone, phosphate bound to the wild-type enzyme is known to be 19 cm-1 lower (at, 1713 cm-1) than that of dihydroxyacetone phosphate free in solution (at, 1732 cm-1), and this decrease in stretching frequency has been ascribed to, an enzymic electrophile that polarizes the substrate carbonyl group toward, the transition state for the enolization. Infrared spectra of substrate, bound to two site-directed mutants of yeast triosephosphate isomerase in, which histidine-95 has been changed to glutamine or to asparagine show, unperturbed carbonyl stretching frequencies between 1732 and 1742 cm-1., The lack of carbonyl polarization when histidine-95 is removed suggests, that histidine-95 is indeed the catalytic electrophile, at least for, dihydroxyacetone phosphate. Kinetic studies of the glutamine mutant (H95Q), have shown that the enzyme follows a subtly different mechanism of proton, transfers involving only a single acid-base catalytic group. These, findings suggest an additional role for histidine-95 as a general, acid-base catalyst in the wild-type enzyme. The X-ray crystal structure of, the H95Q mutant with an intermediate analogue, phosphoglycolohydroxamate, bound at the active site has been solved to 2.8-A resolution, and this, structure clearly implicates glutamate-165, the catalytic base in the, wild-type isomerase, as the sole acid-base catalyst for the mutant, enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
+<StructureSection load='3ypi' size='340' side='right'caption='[[3ypi]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ypi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3YPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3YPI 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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGH:PHOSPHOGLYCOLOHYDROXAMIC+ACID'>PGH</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=3ypi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ypi OCA], [https://pdbe.org/3ypi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ypi RCSB], [https://www.ebi.ac.uk/pdbsum/3ypi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ypi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TPIS_YEAST TPIS_YEAST]
+== 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/yp/3ypi_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=3ypi ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-YPI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with PGH as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3YPI OCA].
+*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95., Komives EA, Chang LC, Lolis E, Tilton RF, Petsko GA, Knowles JR, Biochemistry. 1991 Mar 26;30(12):3011-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2007138 2007138]
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Lolis E]]
-[[Category: Triose-phosphate isomerase]]
+[[Category: Petsko GA]]
-[[Category: Lolis, E.]]
-[[Category: Petsko, G.A.]]
-[[Category: PGH]]
-[[Category: isomerase(intramolecular oxidoreductse)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:01:26 2007''