2xfd: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2xfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XFD FirstGlance]. <br>
<table><tr><td colspan='2'>[[2xfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XFD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.19&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2xfe|2xfe]], [[2xhh|2xhh]], [[2xhj|2xhj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900005:beta-cellobiose'>PRD_900005</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xfd OCA], [https://pdbe.org/2xfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xfd RCSB], [https://www.ebi.ac.uk/pdbsum/2xfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xfd ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xfd OCA], [https://pdbe.org/2xfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xfd RCSB], [https://www.ebi.ac.uk/pdbsum/2xfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xfd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/D7GNB4_9BACT D7GNB4_9BACT]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2xfd ConSurf].
</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=2xfd ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs). Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases that contribute to plant cell wall degradation. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, a member of the CBM60 family, displays a beta-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two beta-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, while binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation that ligand recognition at site 2 requires only a beta-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36), however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. 3-D-structure based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed.
Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules.,Montanier C, Flint JE, Bolam DN, Xie H, Liu Z, Rogowski A, Weiner D, Ratnaparkhe S, Nurizzo D, Roberts SM, Turkenburg JP, Davies GJ, Gilbert HJ J Biol Chem. 2010 Jul 21. PMID:20659893<ref>PMID:20659893</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2xfd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bolam, D N]]
[[Category: Bolam DN]]
[[Category: Davies, G J]]
[[Category: Davies GJ]]
[[Category: Flint, J E]]
[[Category: Flint JE]]
[[Category: Gilbert, H J]]
[[Category: Gilbert HJ]]
[[Category: Liu, Z]]
[[Category: Liu Z]]
[[Category: Montanier, C]]
[[Category: Montanier C]]
[[Category: Nurizzo, D]]
[[Category: Nurizzo D]]
[[Category: Roberts, S M]]
[[Category: Roberts SM]]
[[Category: Rogowski, A]]
[[Category: Rogowski A]]
[[Category: Turkenburg, J P]]
[[Category: Turkenburg JP]]
[[Category: Weiner, D P]]
[[Category: Weiner DP]]
[[Category: Xie, H]]
[[Category: Xie H]]
[[Category: Sugar binding protein]]

Revision as of 10:10, 1 May 2024

vCBM60 in complex with cellobiosevCBM60 in complex with cellobiose

Structural highlights

2xfd is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.19Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D7GNB4_9BACT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

2xfd, resolution 1.19Å

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OCA
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