2xfe

From Proteopedia

(Difference between revisions)

Current revision

vCBM60 in complex with galactobiose

Structural highlights

2xfe 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 1.82Å
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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. J Biol Chem. 2010 Jul 21. PMID:20659893 doi:10.1074/jbc.M110.142133

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xfe"

@@ Line 3: / Line 3: @@
 <StructureSection load='2xfe' size='340' side='right'caption='[[2xfe]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XFE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XFE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xfe]] 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=2XFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XFE FirstGlance]. <br>
-</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=GAL:BETA-D-GALACTOSE'>GAL</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]] 1.82&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xfd|2xfd]], [[2xhh|2xhh]], [[2xhj|2xhj]]</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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PRD_900113:4beta-beta-galactobiose'>PRD_900113</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2xfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xfe OCA], [http://pdbe.org/2xfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xfe RCSB], [http://www.ebi.ac.uk/pdbsum/2xfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xfe 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=2xfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xfe OCA], [https://pdbe.org/2xfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xfe RCSB], [https://www.ebi.ac.uk/pdbsum/2xfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xfe ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D7GNB4_9BACT D7GNB4_9BACT]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xf/2xfe_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[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]]

2xfe

From Proteopedia

Current revision

vCBM60 in complex with galactobiose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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