7tim: Difference between revisions

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-[[Image:7tim.gif|left|200px]]
-<!--
+==STRUCTURE OF THE TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX: AN ANALOGUE OF THE INTERMEDIATE ON THE REACTION PATHWAY==
-The line below this paragraph, containing "STRUCTURE_7tim", creates the "Structure Box" on the page.
+<StructureSection load='7tim' size='340' side='right'caption='[[7tim]], [[Resolution|resolution]] 1.90&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'>[[7tim]] 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=7TIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TIM 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]] 1.9&#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>
-{{STRUCTURE_7tim|  PDB=7tim  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tim OCA], [https://pdbe.org/7tim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tim RCSB], [https://www.ebi.ac.uk/pdbsum/7tim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tim 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/ti/7tim_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=7tim ConSurf].
+<div style="clear:both"></div>
-'''STRUCTURE OF THE TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX: AN ANALOGUE OF THE INTERMEDIATE ON THE REACTION PATHWAY'''
+==See Also==
+*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The glycolytic enzyme triosephosphate isomerase (TIM) catalyzes the interconversion of the three-carbon sugars dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) at a rate limited by the diffusion of substrate to the enzyme. We have solved the three-dimensional structure of TIM complexed with a reactive intermediate analogue, phosphoglycolohydroxamate (PGH), at 1.9-A resolution and have refined the structure to an R-factor of 18%. Analysis of the refined structure reveals the geometry of the active-site residues and the interactions they make with the inhibitor and, by analogy, the substrates. The structure is consistent with an acid-base mechanism in which the carboxylate of Glu-165 abstracts a proton from carbon while His-95 donates a proton to oxygen to form an enediol (or enediolate) intermediate. The conformation of the bound substrate stereoelectronically favors proton transfer from substrate carbon to the syn orbital of Glu-165. The crystal structure suggests that His-95 is neutral rather than cationic in the ground state and therefore would have to function as an imidazole acid instead of the usual imidazolium. Lys-12 is oriented so as to polarize the substrate oxygens by hydrogen bonding and/or electrostatic interaction, providing stabilization for the charged transition state. Asn-10 may play a similar role.
+[[Category: Large Structures]]
-==About this Structure==
-TIM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TIM OCA].
-==Reference==
-Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway., Davenport RC, Bash PA, Seaton BA, Karplus M, Petsko GA, Ringe D, Biochemistry. 1991 Jun 18;30(24):5821-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2043623 2043623]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Bash PA]]
-[[Category: Triose-phosphate isomerase]]
+[[Category: Davenport RC]]
-[[Category: Bash, P A.]]
+[[Category: Karplus M]]
-[[Category: Davenport, R C.]]
+[[Category: Petsko GA]]
-[[Category: Karplus, M.]]
+[[Category: Ringe D]]
-[[Category: Petsko, G A.]]
+[[Category: Seaton BA]]
-[[Category: Ringe, D.]]
-[[Category: Seaton, B A.]]
-[[Category: Intramolecular oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:47:47 2008''