2icx: Difference between revisions

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-[[Image:2icx.gif|left|200px]]
- {{Structure
+==Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP==
-|PDB= 2icx |SIZE=350|CAPTION= <scene name='initialview01'>2icx</scene>, resolution 1.850&Aring;
+<StructureSection load='2icx' size='340' side='right'caption='[[2icx]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=UTP:URIDINE+5&#39;-TRIPHOSPHATE'>UTP</scene>
+<table><tr><td colspan='2'>[[2icx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. 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>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-|GENE= At3g03250, T17B22.6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
+<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>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01704 UDPGP]</span>
+<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>
-|RELATEDENTRY=[[1z90|1Z90]], [[2icy|2ICY]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2icx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2icx OCA], [http://www.ebi.ac.uk/pdbsum/2icx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2icx RCSB]</span>
+== 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 ==
-'''Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ic/2icx_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=2icx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
 The 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.
-==About this Structure==
+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<ref>PMID:17178129</ref>
-ICX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ICX OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17178129 17178129]
+</div>
+<div class="pdbe-citations 2icx" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
+[[Category: Bingman CA]]
-[[Category: Bingman, C A.]]
+[[Category: Bitto E]]
-[[Category: Bitto, E.]]
+[[Category: McCoy JG]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
+[[Category: Phillips Jr GN]]
-[[Category: Jr., G N.Phillips.]]
+[[Category: Wesenberg GE]]
-[[Category: McCoy, J G.]]
-[[Category: Wesenberg, G E.]]
-[[Category: at3g03250]]
-[[Category: center for eukaryotic structural genomic]]
-[[Category: cesg]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: putative udp-glucose pyrophosphorylase]]
-[[Category: structural genomic]]
-[[Category: structural genomics functional follow-up study]]
-[[Category: utp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:42:39 2008''