3ck9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:29, 30 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3ck9.png|left|200px]]
 
-
<!--
+
==B. thetaiotaomicron SusD with maltoheptaose==
-
The line below this paragraph, containing "STRUCTURE_3ck9", creates the "Structure Box" on the page.
+
<StructureSection load='3ck9' size='340' side='right'caption='[[3ck9]], [[Resolution|resolution]] 2.20&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'>[[3ck9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CK9 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]] 2.2&#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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900035:alpha-maltohexaose'>PRD_900035</scene></td></tr>
-
{{STRUCTURE_3ck9| PDB=3ck9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ck9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ck9 OCA], [https://pdbe.org/3ck9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ck9 RCSB], [https://www.ebi.ac.uk/pdbsum/3ck9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ck9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SUSD_BACTN SUSD_BACTN] Major starch-binding protein present at the surface of the cell. Mediates starch-binding before starch transport in the periplasm for degradation.<ref>PMID:10986238</ref> <ref>PMID:11717282</ref> <ref>PMID:18611383</ref> <ref>PMID:9006015</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/ck/3ck9_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3ck9 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique alpha-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.
-
===B. thetaiotaomicron SusD with maltoheptaose===
+
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.,Koropatkin NM, Martens EC, Gordon JI, Smith TJ Structure. 2008 Jul;16(7):1105-15. PMID:18611383<ref>PMID:18611383</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_18611383}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3ck9" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18611383 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18611383}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-
3CK9 is a 2 chains structure of 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=3CK9 OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Gordon JI]]
-
==Reference==
+
[[Category: Koropatkin NM]]
-
<ref group="xtra">PMID:18611383</ref><references group="xtra"/>
+
[[Category: Martens EC]]
-
[[Category: Bacteroides thetaiotaomicron]]
+
[[Category: Smith TJ]]
-
[[Category: Gordon, J I.]]
+
-
[[Category: Koropatkin, N M.]]
+
-
[[Category: Martens, E C.]]
+
-
[[Category: Smith, T J.]]
+
-
[[Category: Carbohydrate binding]]
+
-
[[Category: Starch binding]]
+
-
[[Category: Sugar binding protein]]
+
-
[[Category: Tpr repeat]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:01:30 2009''
+

Current revision

B. thetaiotaomicron SusD with maltoheptaose

PDB ID 3ck9

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ck9"
Personal tools