2icx: Difference between revisions

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-{{Seed}}
-[[Image:2icx.png|left|200px]]
-<!--
+==Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP==
-The line below this paragraph, containing "STRUCTURE_2icx", creates the "Structure Box" on the page.
+<StructureSection load='2icx' size='340' side='right'caption='[[2icx]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_2icx|  PDB=2icx  |  SCENE=  }}
+<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>
+== 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 ==
+[[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/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.
-===Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17178129}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2icx" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17178129 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17178129}}
+__TOC__
+</StructureSection>
-==About this Structure==
-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==
-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]
 [[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 Jul 28 01:42:55 2008''