2xbd: Difference between revisions

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{{Seed}}
[[Image:2xbd.png|left|200px]]


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==INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, NMR, MINIMIZED AVERAGE STRUCTURE==
The line below this paragraph, containing "STRUCTURE_2xbd", creates the "Structure Box" on the page.
<StructureSection load='2xbd' size='340' side='right'caption='[[2xbd]]' 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'>[[2xbd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XBD 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">Solution NMR, 1 model</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xbd OCA], [https://pdbe.org/2xbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xbd RCSB], [https://www.ebi.ac.uk/pdbsum/2xbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xbd ProSAT]</span></td></tr>
{{STRUCTURE_2xbd|  PDB=2xbd  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/XYND_CELFI XYND_CELFI] Endo-acting xylanase which displays no detectable activity against polysaccharides other than xylan. Hydrolyzes glucosidic bonds with retention of anomeric configuration.
== 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/xb/2xbd_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=2xbd ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Many enzymes that digest polysaccharides contain separate polysaccharide-binding domains. Structures have been previously determined for a number of cellulose-binding domains (CBDs) from cellulases. RESULTS: The family IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan but not cellulose. Its structure is similar to that of the homologous family IIa CBD from C. fimi Cex, consisting of two four-stranded beta sheets that form a twisted 'beta sandwich'. The xylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar residues. CONCLUSIONS: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplanar, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary structures of the ligands cellulose and xylan. XBD1 and CexCBD represent a striking example of two proteins that have high sequence similarity but a different function.


===INTERNAL XYLAN BINDING DOMAIN FROM CELLULOMONAS FIMI XYLANASE D, NMR, MINIMIZED AVERAGE STRUCTURE===
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.,Simpson PJ, Bolam DN, Cooper A, Ciruela A, Hazlewood GP, Gilbert HJ, Williamson MP Structure. 1999 Jul 15;7(7):853-64. PMID:10425686<ref>PMID:10425686</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_10425686}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2xbd" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 10425686 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_10425686}}
__TOC__
 
</StructureSection>
==About this Structure==
2XBD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XBD OCA].
 
==Reference==
A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity., Simpson PJ, Bolam DN, Cooper A, Ciruela A, Hazlewood GP, Gilbert HJ, Williamson MP, Structure. 1999 Jul 15;7(7):853-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10425686 10425686]
[[Category: Cellulomonas fimi]]
[[Category: Cellulomonas fimi]]
[[Category: Endo-1,4-beta-xylanase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Bolam DN]]
[[Category: Bolam, D N.]]
[[Category: Ciruela A]]
[[Category: Ciruela, A.]]
[[Category: Cooper A]]
[[Category: Cooper, A.]]
[[Category: Gilbert HJ]]
[[Category: Gilbert, H J.]]
[[Category: Hazlewood GP]]
[[Category: Hazlewood, G P.]]
[[Category: Simpson PJ]]
[[Category: Simpson, P J.]]
[[Category: Williamson MP]]
[[Category: Williamson, M P.]]
[[Category: Beta-sheet]]
[[Category: Hydrolase]]
[[Category: Xylan binding domain]]
[[Category: Xylanase]]
 
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Retrieved from "https://proteopedia.org/2xbd"