2x16: Difference between revisions
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< | ==Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase== | ||
<StructureSection load='2x16' size='340' side='right'caption='[[2x16]], [[Resolution|resolution]] 2.13Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2x16]] 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=2X16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X16 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]] 2.13Å</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=2x16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x16 OCA], [https://pdbe.org/2x16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x16 RCSB], [https://www.ebi.ac.uk/pdbsum/2x16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x16 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/x1/2x16_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=2x16 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Crystallographic binding studies have been carried out to probe the active-site binding properties of a monomeric variant (A-TIM) of triosephosphate isomerase (TIM). These binding studies are part of a structure-based directed-evolution project aimed towards changing the substrate specificity of monomeric TIM and are therefore aimed at finding binders which are substrate-like molecules. A-TIM has a modified more extended binding pocket between loop-7 and loop-8 compared with wild-type TIM. The A-TIM crystals were grown in the presence of citrate, which is bound in the active site of each of the two molecules in the asymmetric unit. In this complex, the active-site loops loop-6 and loop-7 adopt the closed conformation, similar to that observed in liganded wild-type TIM. Extensive crystal-soaking protocols have been developed to flush the bound citrate out of the active-site pocket of both molecules and the crystal structure shows that the unliganded open conformation of the A-TIM active site is the same as in unliganded wild-type TIM. It is also shown that sulfonate compounds corresponding to the transition-state analogue 2-phosphoglycolate bind in the active site, which has a closed conformation. It is also shown that the new binding pocket of A-TIM can bind 3-phosphoglycerate (3PGA; an analogue of a C4-sugar phosphate) and 4-phospho-D-erythronohydroxamic acid (4PEH; an analogue of a C5-sugar phosphate). Therefore, these studies have provided a rationale for starting directed-evolution experiments aimed at generating the catalytic properties of a C5-sugar phosphate isomerase on the A-TIM framework. | |||
Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase.,Salin M, Kapetaniou EG, Vaismaa M, Lajunen M, Casteleijn MG, Neubauer P, Salmon L, Wierenga RK Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):934-44. Epub 2010, Jul 14. PMID:20693693<ref>PMID:20693693</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2x16" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | |||
== | |||
< | |||
[[Category: | |||
[[Category: Trypanosoma brucei brucei]] | [[Category: Trypanosoma brucei brucei]] | ||
[[Category: Casteleijn | [[Category: Casteleijn MG]] | ||
[[Category: Kapetaniou | [[Category: Kapetaniou EG]] | ||
[[Category: Lajunen | [[Category: Lajunen M]] | ||
[[Category: Neubauer | [[Category: Neubauer P]] | ||
[[Category: Salin | [[Category: Salin M]] | ||
[[Category: Salmon | [[Category: Salmon L]] | ||
[[Category: Vaismaa | [[Category: Vaismaa M]] | ||
[[Category: Wierenga | [[Category: Wierenga R]] | ||
Latest revision as of 13:21, 20 December 2023
Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomeraseCrystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedCrystallographic binding studies have been carried out to probe the active-site binding properties of a monomeric variant (A-TIM) of triosephosphate isomerase (TIM). These binding studies are part of a structure-based directed-evolution project aimed towards changing the substrate specificity of monomeric TIM and are therefore aimed at finding binders which are substrate-like molecules. A-TIM has a modified more extended binding pocket between loop-7 and loop-8 compared with wild-type TIM. The A-TIM crystals were grown in the presence of citrate, which is bound in the active site of each of the two molecules in the asymmetric unit. In this complex, the active-site loops loop-6 and loop-7 adopt the closed conformation, similar to that observed in liganded wild-type TIM. Extensive crystal-soaking protocols have been developed to flush the bound citrate out of the active-site pocket of both molecules and the crystal structure shows that the unliganded open conformation of the A-TIM active site is the same as in unliganded wild-type TIM. It is also shown that sulfonate compounds corresponding to the transition-state analogue 2-phosphoglycolate bind in the active site, which has a closed conformation. It is also shown that the new binding pocket of A-TIM can bind 3-phosphoglycerate (3PGA; an analogue of a C4-sugar phosphate) and 4-phospho-D-erythronohydroxamic acid (4PEH; an analogue of a C5-sugar phosphate). Therefore, these studies have provided a rationale for starting directed-evolution experiments aimed at generating the catalytic properties of a C5-sugar phosphate isomerase on the A-TIM framework. Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase.,Salin M, Kapetaniou EG, Vaismaa M, Lajunen M, Casteleijn MG, Neubauer P, Salmon L, Wierenga RK Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):934-44. Epub 2010, Jul 14. PMID:20693693[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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