2riz: Difference between revisions

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 ==Unliganded B-specific-1,3-galactosyltransferase G176R mutant (ABBB)==
-<StructureSection load='2riz' size='340' side='right' caption='[[2riz]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='2riz' size='340' side='right'caption='[[2riz]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2riz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RIZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2riz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RIZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RIZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rit|2rit]], [[2rix|2rix]], [[2riy|2riy]], [[2rj0|2rj0]], [[2rj1|2rj1]], [[2rj4|2rj4]], [[2rj5|2rj5]], [[2rj6|2rj6]], [[2rj7|2rj7]], [[2rj8|2rj8]], [[2rj9|2rj9]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ABO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2riz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2riz OCA], [https://pdbe.org/2riz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2riz RCSB], [https://www.ebi.ac.uk/pdbsum/2riz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2riz ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fucosylgalactoside_3-alpha-galactosyltransferase Fucosylgalactoside 3-alpha-galactosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.37 2.4.1.37] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2riz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2riz OCA], [http://pdbe.org/2riz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2riz RCSB], [http://www.ebi.ac.uk/pdbsum/2riz PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BGAT_HUMAN BGAT_HUMAN]] This protein is the basis of the ABO blood group system. The histo-blood group ABO involves three carbohydrate antigens: A, B, and H. A, B, and AB individuals express a glycosyltransferase activity that converts the H antigen to the A antigen (by addition of UDP-GalNAc) or to the B antigen (by addition of UDP-Gal), whereas O individuals lack such activity.
+[https://www.uniprot.org/uniprot/BGAT_HUMAN BGAT_HUMAN] This protein is the basis of the ABO blood group system. The histo-blood group ABO involves three carbohydrate antigens: A, B, and H. A, B, and AB individuals express a glycosyltransferase activity that converts the H antigen to the A antigen (by addition of UDP-GalNAc) or to the B antigen (by addition of UDP-Gal), whereas O individuals lack such activity.
 == 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/ri/2riz_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2riz_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=2riz ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed by two closely related glycosyltransferases, an alpha-(1--&gt;3)-N-acetylgalactosaminyltransferase (GTA) and an alpha-(1--&gt;3)-galactosyltransferase (GTB). Of their 354 amino acid residues, GTA and GTB differ by only four "critical" residues. High resolution structures for GTB and the GTA/GTB chimeric enzymes GTB/G176R and GTB/G176R/G235S bound to a panel of donor and acceptor analog substrates reveal "open," "semi-closed," and "closed" conformations as the enzymes go from the unliganded to the liganded states. In the open form the internal polypeptide loop (amino acid residues 177-195) adjacent to the active site in the unliganded or H antigen-bound enzymes is composed of two alpha-helices spanning Arg(180)-Met(186) and Arg(188)-Asp(194), respectively. The semi-closed and closed forms of the enzymes are generated by binding of UDP or of UDP and H antigen analogs, respectively, and show that these helices merge to form a single distorted helical structure with alternating alpha-3(10)-alpha character that partially occludes the active site. The closed form is distinguished from the semi-closed form by the ordering of the final nine C-terminal residues through the formation of hydrogen bonds to both UDP and H antigen analogs. The semi-closed forms for various mutants generally show significantly more disorder than the open forms, whereas the closed forms display little or no disorder depending strongly on the identity of residue 176. Finally, the use of synthetic analogs reveals how H antigen acceptor binding can be critical in stabilizing the closed conformation. These structures demonstrate a delicately balanced substrate recognition mechanism and give insight on critical aspects of donor and acceptor specificity, on the order of substrate binding, and on the requirements for catalysis.
-ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes.,Alfaro JA, Zheng RB, Persson M, Letts JA, Polakowski R, Bai Y, Borisova SN, Seto NO, Lowary TL, Palcic MM, Evans SV J Biol Chem. 2008 Apr 11;283(15):10097-108. Epub 2008 Jan 11. PMID:18192272<ref>PMID:18192272</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2riz" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Glycosyltransferase|Glycosyltransferase]]
+*[[Glycosyltransferase 3D structures|Glycosyltransferase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Fucosylgalactoside 3-alpha-galactosyltransferase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[Category: Large Structures]]
-[[Category: Alfaro, J A]]
+[[Category: Alfaro JA]]
-[[Category: Evans, S V]]
+[[Category: Evans SV]]
-[[Category: Blood group antigen]]
-[[Category: Glycoprotein]]
-[[Category: Glycosyltransferase]]
-[[Category: Golgi apparatus]]
-[[Category: Gtb abo rossman fold bbbb unliganded]]
-[[Category: Manganese]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Secreted]]
-[[Category: Signal-anchor]]
-[[Category: Transferase]]
-[[Category: Transmembrane]]