3ug3: Difference between revisions

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-[[Image:3ug3.jpg|left|200px]]
-<!--
+==Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form==
-The line below this paragraph, containing "STRUCTURE_3ug3", creates the "Structure Box" on the page.
+<StructureSection load='3ug3' size='340' side='right'caption='[[3ug3]], [[Resolution|resolution]] 1.80&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'>[[3ug3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UG3 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-{{STRUCTURE_3ug3|  PDB=3ug3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ug3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ug3 OCA], [https://pdbe.org/3ug3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ug3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ug3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ug3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WYB7_THEMA Q9WYB7_THEMA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+alpha-L-Arabinofuranosidase from the hyperthermophilic bacterium Thermotoga maritima (Tm-AFase) is an extremely thermophilic enzyme belonging to glycoside hydrolase family 51. It can catalyze the transglycosylation of a novel glycosyl donor, 4,6-dimethoxy-1,3,5-triazin-2-yl (DMT)-beta-D-xylopyranoside. In this study we determined the crystal structures of Tm-AFase in substrate-free and complex forms with arabinose and xylose at 1.8-2.3 A resolution to determine the architecture of the substrate binding pocket. Subsite -1 of Tm-AFase is similar to that of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus, but the substrate binding pocket of Tm-AFase is narrower and more hydrophobic. Possible substrate binding modes were investigated by automated docking analysis.
-===Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form===
+Crystal Structures of Glycoside Hydrolase Family 51 alpha-L-Arabinofuranosidase from Thermotoga maritima.,Im DH, Kimura K, Hayasaka F, Tanaka T, Noguchi M, Kobayashi A, Shoda S, Miyazaki K, Wakagi T, Fushinobu S Biosci Biotechnol Biochem. 2012 Feb 23;76(2):423-8. Epub 2012 Feb 7. PMID:22313787<ref>PMID:22313787</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_22313787}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3ug3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22313787 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22313787}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3ug3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UG3 OCA].
-==Reference==
-<ref group="xtra">PMID:022313787</ref><ref group="xtra">PMID:015965714</ref><references group="xtra"/>
-[[Category: Alpha-N-arabinofuranosidase]]
 [[Category: Thermotoga maritima]]
-[[Category: Fushinobu, S.]]
+[[Category: Fushinobu S]]
-[[Category: Im, D H.]]
+[[Category: Im D-H]]
-[[Category: Miyazaki, K.]]
+[[Category: Miyazaki K]]
-[[Category: Wakagi, T.]]
+[[Category: Wakagi T]]
-[[Category: Hydrolase]]
-[[Category: Tim barrel]]