2zag: Difference between revisions

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-{{Seed}}
-[[Image:2zag.png|left|200px]]
-<!--
+==Crystal structure of the SeMet-substituted soluble domain of STT3 from P. furiosus==
-The line below this paragraph, containing "STRUCTURE_2zag", creates the "Structure Box" on the page.
+<StructureSection load='2zag' size='340' side='right'caption='[[2zag]], [[Resolution|resolution]] 3.00&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'>[[2zag]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZAG 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2zag|  PDB=2zag  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zag OCA], [https://pdbe.org/2zag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zag RCSB], [https://www.ebi.ac.uk/pdbsum/2zag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zag ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGLB1_PYRFU AGLB1_PYRFU] Oligosaccharyl transferase (OST) that catalyzes the initial transfer of a defined glycan (ManNAcXyl(2)GlcAMan(2)GalNAc in P.furiosus) from the lipid carrier dolichol-monophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation.<ref>PMID:18046457</ref>
+== 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/za/2zag_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=2zag ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Asn-glycosylation is widespread not only in eukaryotes but also in archaea and some eubacteria. Oligosaccharyltransferase (OST) catalyzes the co-translational transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. Here, we report that a thermophilic archaeon, Pyrococcus furiosus OST is composed of the STT3 protein alone, and catalyzes the transfer of a heptasaccharide, containing one hexouronate and two pentose residues, onto peptides in an Asn-X-Thr/Ser-motif-dependent manner. We also determined the 2.7-A resolution crystal structure of the C-terminal soluble domain of Pyrococcus STT3. The structure-based multiple sequence alignment revealed a new motif, DxxK, which is adjacent to the well-conserved WWDYG motif in the tertiary structure. The mutagenesis of the DK motif residues in yeast STT3 revealed the essential role of the motif in the catalytic activity. The function of this motif may be related to the binding of the pyrophosphate group of lipid-linked oligosaccharide donors through a transiently bound cation. Our structure provides the first structural insights into the formation of the oligosaccharide-asparagine bond.
-===Crystal structure of the SeMet-substituted soluble domain of STT3 from P. furiosus===
+Structure-guided identification of a new catalytic motif of oligosaccharyltransferase.,Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D EMBO J. 2008 Jan 9;27(1):234-43. Epub 2007 Nov 29. PMID:18046457<ref>PMID:18046457</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_18046457}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2zag" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18046457 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18046457}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ZAG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAG OCA].
+[[Category: Pyrococcus furiosus DSM 3638]]
+[[Category: Maita N]]
-==Reference==
-Structure-guided identification of a new catalytic motif of oligosaccharyltransferase., Igura M, Maita N, Kamishikiryo J, Yamada M, Obita T, Maenaka K, Kohda D, EMBO J. 2008 Jan 9;27(1):234-43. Epub 2007 Nov 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18046457 18046457]
-[[Category: Pyrococcus furiosus]]
-[[Category: Single protein]]
-[[Category: Maita, N.]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:53:48 2008''