2am5: Difference between revisions

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-[[Image:2am5.png|left|200px]]
-{{STRUCTURE_2am5|  PDB=2am5  |  SCENE=  }}
+==Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP==
+<StructureSection load='2am5' size='340' side='right'caption='[[2am5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2am5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AM5 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]] 1.6&#8491;</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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></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=2am5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2am5 OCA], [https://pdbe.org/2am5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2am5 RCSB], [https://www.ebi.ac.uk/pdbsum/2am5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2am5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MGAT1_RABIT MGAT1_RABIT] Initiates complex N-linked carbohydrate formation. Essential for the conversion of high-mannose to hybrid and complex N-glycans.
+== 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/am/2am5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2am5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Golgi-resident glycosyltransferase, UDP-N-acetyl-d-glucosamine:alpha-3-d-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I), initiates the conversion of high-mannose oligosaccharides to complex and hybrid structures in the biosynthesis of N-linked glycans. Reported here are the X-ray crystal structures of GnT I in complex with UDP-CH2-GlcNAc (a non-hydrolyzable C-glycosidic phosphonate), UDP-2-deoxy-2-fluoro-glucose, UDP-glucose and UDP. Collectively, these structures provide evidence for the importance of the GlcNAc moiety and its N-acetyl group in donor substrate binding, as well as insight into the role played by the flexible 318-330 loop in substrate binding and product release. In addition, the UDP-CH2-GlcNAc complex reveals a well-defined glycerol molecule poised for nucleophilic attack on the C1 atom of the donor substrate analogue. The position and orientation of this glycerol molecule have allowed us to model the binding of the Manalpha1,3Manbeta1 moiety of the acceptor substrate and, based on the model, to suggest a rationalization for the main determinants of GnT I acceptor specificity.
-===Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP===
+X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.,Gordon RD, Sivarajah P, Satkunarajah M, Ma D, Tarling CA, Vizitiu D, Withers SG, Rini JM J Mol Biol. 2006 Jun 30;360(1):67-79. Epub 2006 May 12. PMID:16769084<ref>PMID:16769084</ref>
-{{ABSTRACT_PUBMED_16769084}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2am5" style="background-color:#fffaf0;"></div>
-[[2am5]] is a 1 chain structure of [[O-GlcNAc transferase]] with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AM5 OCA].
 ==See Also==
-*[[O-GlcNAc transferase|O-GlcNAc transferase]]
+*[[O-GlcNAc transferase 3D structures|O-GlcNAc transferase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016769084</ref><references group="xtra"/>
+__TOC__
-[[Category: Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Gordon, R D.]]
+[[Category: Gordon RD]]
-[[Category: Rini, J M.]]
+[[Category: Rini JM]]
-[[Category: Glycosyltransferase]]
-[[Category: N-acetylglucosaminyltransferase]]
-[[Category: Transferase]]
-[[Category: Udp]]
-[[Category: Udp-glcnac]]