3k8m: Difference between revisions

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-{{Seed}}
-[[Image:3k8m.jpg|left|200px]]
-<!--
+==Crystal structure of SusG with acarbose==
-The line below this paragraph, containing "STRUCTURE_3k8m", creates the "Structure Box" on the page.
+<StructureSection load='3k8m' size='340' side='right'caption='[[3k8m]], [[Resolution|resolution]] 2.50&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'>[[3k8m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K8M 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene>, <scene name='pdbligand=PRD_900007:alpha-acarbose'>PRD_900007</scene>, <scene name='pdbligand=PRD_900110:acarbose-derived+trisaccharide'>PRD_900110</scene></td></tr>
-{{STRUCTURE_3k8m|  PDB=3k8m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k8m OCA], [https://pdbe.org/3k8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k8m RCSB], [https://www.ebi.ac.uk/pdbsum/3k8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k8m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SUSG_BACTN SUSG_BACTN] Alpha-amylase that cleaves starch into oligosaccharides before internalization for degradation, the first step in starch degradation.<ref>PMID:10572122</ref> <ref>PMID:11717282</ref> <ref>PMID:20159465</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/k8/3k8m_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=3k8m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+SusG is an alpha-amylase and part of a large protein complex on the outer surface of the bacterial cell and plays a major role in carbohydrate acquisition by the animal gut microbiota. Presented here, the atomic structure of SusG has an unusual extended, bilobed structure composed of amylase at one end and an unprecedented internal carbohydrate-binding motif at the other. Structural studies further demonstrate that the carbohydrate-binding motif binds maltooligosaccharide distal to, and on the opposite side of, the amylase catalytic site. SusG has an additional starch-binding site on the amylase domain immediately adjacent to the active cleft. Mutagenesis analysis demonstrates that these two additional starch-binding sites appear to play a role in catabolism of insoluble starch. However, elimination of these sites has only a limited effect, suggesting that they may have a more important role in product exchange with other Sus components.
-===Crystal structure of SusG with acarbose===
+SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.,Koropatkin NM, Smith TJ Structure. 2010 Feb 10;18(2):200-15. PMID:20159465<ref>PMID:20159465</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3k8m" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20159465}}, adds the Publication Abstract to the page
+*[[Amylase 3D structures|Amylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20159465 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20159465}}
+__TOC__
+</StructureSection>
-==About this Structure==
-K8M is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K8M OCA].
-==Reference==
-<ref group="xtra">PMID:20159465</ref><references group="xtra"/>
 [[Category: Bacteroides thetaiotaomicron]]
-[[Category: Koropatkin, N M.]]
+[[Category: Large Structures]]
-[[Category: Smith, T J.]]
+[[Category: Koropatkin NM]]
-[[Category: Alpha8/beta8 barrel]]
+[[Category: Smith TJ]]
-[[Category: Amylase]]
-[[Category: Beta-sandwich]]
-[[Category: Cbm]]
-[[Category: Membrane protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar  3 15:59:14 2010''