2icx: Difference between revisions
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==Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP== | ==Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP== | ||
<StructureSection load='2icx' size='340' side='right' caption='[[2icx]], [[Resolution|resolution]] 1.85Å' scene=''> | <StructureSection load='2icx' size='340' side='right'caption='[[2icx]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2icx]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2icx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ICX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ICX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z90|1z90]], [[2icy|2icy]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1z90|1z90]], [[2icy|2icy]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g03250, T17B22.6 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g03250, T17B22.6 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2icx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2icx OCA], [https://pdbe.org/2icx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2icx RCSB], [https://www.ebi.ac.uk/pdbsum/2icx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2icx ProSAT], [https://www.topsan.org/Proteins/CESG/2icx TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/UGPA2_ARATH UGPA2_ARATH]] Plays a central role as a glucosyl donor in cellular metabolic pathways (By similarity). | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Arath]] | [[Category: Arath]] | ||
[[Category: Large Structures]] | |||
[[Category: UTP--glucose-1-phosphate uridylyltransferase]] | [[Category: UTP--glucose-1-phosphate uridylyltransferase]] | ||
[[Category: Bingman, C A]] | [[Category: Bingman, C A]] | ||
Revision as of 14:13, 31 March 2021
Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTPCrystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP
Structural highlights
Function[UGPA2_ARATH] Plays a central role as a glucosyl donor in cellular metabolic pathways (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Angstroms. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Angstroms and 1.85 Angstroms. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal beta-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide-binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed initially to model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity. Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP.,McCoy JG, Bitto E, Bingman CA, Wesenberg GE, Bannen RM, Kondrashov DA, Phillips GN Jr J Mol Biol. 2007 Feb 23;366(3):830-41. Epub 2006 Nov 21. PMID:17178129[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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