2ypi: Difference between revisions

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-[[Image:2ypi.jpg|left|200px]]
- {{Structure
+==CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS==
-|PDB= 2ypi |SIZE=350|CAPTION= <scene name='initialview01'>2ypi</scene>, resolution 2.5&Aring;
+<StructureSection load='2ypi' size='340' side='right'caption='[[2ypi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC ACID'>PGA</scene>
+<table><tr><td colspan='2'>[[2ypi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The February 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''The Glycolytic Enzymes''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_2 10.2210/rcsb_pdb/mom_2004_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YPI FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</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=2ypi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ypi OCA], [https://pdbe.org/2ypi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ypi RCSB], [https://www.ebi.ac.uk/pdbsum/2ypi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ypi 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/2ypi_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=2ypi ConSurf].
+<div style="clear:both"></div>
-'''CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS'''
+==See Also==
+*[[Triose Phosphate Isomerase|Triose Phosphate Isomerase]]
+*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
-==Overview==
+__TOC__
-The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a final R factor of 0.18. The interactions between the inhibitor and enzyme have been analyzed. The inhibitor forms hydrogen bonds to the side chains of His 95 and Glu 165. The latter hydrogen bond confirms that Glu 165 is protonated upon PGA binding. The structure of the complexed enzyme has been compared to that of the unbound form of the enzyme, and conformational changes have been observed: the side chain of Glu 165 moves over 2 A and a 10-residue flexible loop moves over 7 A to close over the active site. Spectroscopic results of phosphoglycolic acid binding to triosephosphate isomerase that have been amassed over the years are also explained in structural terms. The implications for catalysis are noted.
+</StructureSection>
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: RCSB PDB Molecule of the Month]]
-YPI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The following page contains interesting information on the relation of 2YPI with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb50_1.html The Glycolytic Enzymes]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPI OCA].
-==Reference==
-Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis., Lolis E, Petsko GA, Biochemistry. 1990 Jul 17;29(28):6619-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2204418 2204418]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
 [[Category: The Glycolytic Enzymes]]
-[[Category: Triose-phosphate isomerase]]
+[[Category: Lolis E]]
-[[Category: Lolis, E.]]
+[[Category: Petsko GA]]
-[[Category: Petsko, G A.]]
-[[Category: PGA]]
-[[Category: triose phosphate isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:48:22 2008''