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New page: left|200px {{Structure |PDB= 3ckb |SIZE=350|CAPTION= <scene name='initialview01'>3ckb</scene>, resolution 2.300Å |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+...
 
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[[Image:3ckb.jpg|left|200px]]


{{Structure
==B. thetaiotaomicron SusD with maltotriose==
|PDB= 3ckb |SIZE=350|CAPTION= <scene name='initialview01'>3ckb</scene>, resolution 2.300&Aring;
<StructureSection load='3ckb' size='340' side='right'caption='[[3ckb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+600'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+700'>AC2</scene>, <scene name='pdbsite=AC3:Mlr+Binding+Site+For+Residue+A+903'>AC3</scene> and <scene name='pdbsite=AC4:Mlr+Binding+Site+For+Residue+B+904'>AC4</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MLR:MALTOTRIOSE'>MLR</scene>
<table><tr><td colspan='2'>[[3ckb]] 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=3CKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CKB FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
|GENE= SusD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 Bacteroides thetaiotaomicron])
<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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900009:alpha-maltotriose'>PRD_900009</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07980 SusD_RagB]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ckb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckb OCA], [https://pdbe.org/3ckb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ckb RCSB], [https://www.ebi.ac.uk/pdbsum/3ckb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckb ProSAT]</span></td></tr>
|RELATEDENTRY=[[3ck7|3CK7]], [[3ck8|3CK8]], [[3ck9|3CK9]], [[3ckc|3CKC]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ckb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckb OCA], [http://www.ebi.ac.uk/pdbsum/3ckb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3ckb RCSB]</span>
== 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/3ckb_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=3ckb 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 maltotriose'''
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>
==About this Structure==
</div>
3CKB is a [[Single protein]] structure of sequence 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=3CKB OCA].
<div class="pdbe-citations 3ckb" style="background-color:#fffaf0;"></div>
[[Category: Bacteroides thetaiotaomicron]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Gordon, J I.]]
__TOC__
[[Category: Koropatkin, N M.]]
</StructureSection>
[[Category: Martens, E C.]]
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
[[Category: Smith, T J.]]
[[Category: Large Structures]]
[[Category: carbohydrate binding]]
[[Category: Gordon JI]]
[[Category: starch binding]]
[[Category: Koropatkin NM]]
[[Category: sugar binding protein]]
[[Category: Martens EC]]
[[Category: tpr repeat]]
[[Category: Smith TJ]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 12:00:18 2008''

Latest revision as of 12:29, 30 August 2023

B. thetaiotaomicron SusD with maltotriose

3ckb, resolution 2.30Å

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