2vel: Difference between revisions

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-[[Image:2vel.jpg|left|200px]]
- {{Structure
+==Structure-based enzyme engineering efforts with an inactive monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties==
-|PDB= 2vel |SIZE=350|CAPTION= <scene name='initialview01'>2vel</scene>, resolution 2.30&Aring;
+<StructureSection load='2vel' size='340' side='right'caption='[[2vel]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Cl+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cl+Binding+Site+For+Chain+B'>AC2</scene>, <scene name='pdbsite=AC3:Pga+Binding+Site+For+Chain+B'>AC3</scene> and <scene name='pdbsite=AC4:Pga+Binding+Site+For+Chain+A'>AC4</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene> and <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene>
+<table><tr><td colspan='2'>[[2vel]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VEL 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]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=2vel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vel OCA], [https://pdbe.org/2vel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vel RCSB], [https://www.ebi.ac.uk/pdbsum/2vel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vel ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
+== 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/ve/2vel_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=2vel ConSurf].
+<div style="clear:both"></div>
-'''STRUCTURE-BASED ENZYME ENGINEERING EFFORTS WITH AN INACTIVE MONOMERIC TIM VARIANT: THE IMPORTANCE OF A SINGLE POINT MUTATION FOR GENERATING AN ACTIVE SITE WITH SUITABLE BINDING PROPERTIES'''
+==See Also==
+*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-A monomeric variant of triosephosphate isomerase (TIM) with a new engineered binding groove has been characterized further. In this variant (ml8bTIM), the phosphate binding loop had been shortened, causing the binding site to be much more extended. Here, it is reported that in the V233A variant of ml8bTIM (A-TIM), three important properties of the wild-type TIM active site have been restored: (i) the structural properties of loop-7, (ii) the binding site of a conserved water molecule between loop-7 and loop-8 and (iii) the binding site of the phosphate moiety. It is shown that the active site of A-TIM can bind TIM transition state analogs and suicide inhibitors competently. It is found that the active site geometry of the A-TIM complexes is less compact and more solvent exposed, as in wild-type TIM. This correlates with the observation that the catalytic efficiency of A-TIM for interconverting the TIM substrates is too low to be detected. It is also shown that the A-TIM active site can bind compounds which do not bind to wild-type TIM and which are completely different from the normal TIM substrate, like a citrate molecule. The binding of this citrate molecule is stabilized by hydrogen bonding interactions with the new binding groove.
+[[Category: Large Structures]]
-==About this Structure==
-VEL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEL OCA].
-==Reference==
-Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties., Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P, Wierenga RK, Protein Eng Des Sel. 2008 Jan 31;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18239072 18239072]
-[[Category: Single protein]]
-[[Category: Triose-phosphate isomerase]]
 [[Category: Trypanosoma brucei brucei]]
-[[Category: Alahuhta, M.]]
+[[Category: Alahuhta M]]
-[[Category: Augustyns, K.]]
+[[Category: Augustyns K]]
-[[Category: Casteleijn, M G.]]
+[[Category: Casteleijn MG]]
-[[Category: El-Sayed, I.]]
+[[Category: El-Sayed I]]
-[[Category: Kemmer, C.]]
+[[Category: Kemmer C]]
-[[Category: Neubauer, P.]]
+[[Category: Neubauer P]]
-[[Category: Salin, M.]]
+[[Category: Salin M]]
-[[Category: Wierenga, R K.]]
+[[Category: Wierenga RK]]
-[[Category: CL]]
-[[Category: PGA]]
-[[Category: binding pocket]]
-[[Category: engineering]]
-[[Category: enzyme]]
-[[Category: fatty acid biosynthesis]]
-[[Category: gluconeogenesis]]
-[[Category: glycolysis]]
-[[Category: glycosome]]
-[[Category: isomerase]]
-[[Category: lipid synthesis]]
-[[Category: monomeric]]
-[[Category: pentose shunt]]
-[[Category: substrate specificity]]
-[[Category: tim]]
-[[Category: tim barrel]]
-[[Category: triosephosphate isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:45:42 2008''