This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1w0n

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of uncomplexed Carbohydrate Binding Domain CBM36

Structural highlights

1w0n is a 1 chain structure with sequence from Paenibacillus polymyxa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYND_PAEPO Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation (By similarity). Preferres wheat flour xylan over oat spelt xylan as substrate. Does not display endoxylanase activity.

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 enzymatic degradation of polysaccharides harnesses multimodular enzymes whose carbohydrate binding modules (CBM) target the catalytic domain onto the recalcitrant substrate. Here we report the ab initio structure determination and subsequent refinement, at 0.8 A resolution, of the CBM36 domain of the Paenibacillus polymyxa xylanase 43A. Affinity electrophoresis, isothermal titration calorimetry, and UV difference spectroscopy demonstrate that CBM36 is a novel Ca(2+)-dependent xylan binding domain. The 3D structure of CBM36 in complex with xylotriose and Ca(2+), at 1.5 A resolution, displays significant conformational changes compared to the native structure and reveals the molecular basis for its unique Ca(2+)-dependent binding of xylooligosaccharides through coordination of the O2 and O3 hydroxyls. CBM36 is one of an emerging spectrum of carbohydrate binding modules that increasingly find applications in industry and display great potential for mapping the "glyco-architecture" of plant cells.

Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules.,Jamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VM, Davies GJ Structure. 2004 Jul;12(7):1177-87. PMID:15242594^[1]

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

References

↑ Jamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VM, Davies GJ. Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules. Structure. 2004 Jul;12(7):1177-87. PMID:15242594 doi:10.1016/j.str.2004.04.022

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/1w0n"

Categories: Large Structures | Paenibacillus polymyxa | Boraston AB | Davies GJ | Jamal S

@@ Line 3: / Line 3: @@
 <StructureSection load='1w0n' size='340' side='right'caption='[[1w0n]], [[Resolution|resolution]] 0.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1w0n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aerobacillus_polymyxa"_(prazmowski_1880)_donker_1926 "aerobacillus polymyxa" (prazmowski 1880) donker 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W0N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1w0n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_polymyxa Paenibacillus polymyxa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W0N 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 0.8&#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;'>[[1ux7|1ux7]]</div></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1w0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w0n OCA], [https://pdbe.org/1w0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w0n RCSB], [https://www.ebi.ac.uk/pdbsum/1w0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w0n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/XYND_PAEPO XYND_PAEPO]] Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation (By similarity). Preferres wheat flour xylan over oat spelt xylan as substrate. Does not display endoxylanase activity.
+[https://www.uniprot.org/uniprot/XYND_PAEPO XYND_PAEPO] Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation (By similarity). Preferres wheat flour xylan over oat spelt xylan as substrate. Does not display endoxylanase activity.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Endo-1,4-beta-xylanase]]
 [[Category: Large Structures]]
-[[Category: Boraston, A B]]
+[[Category: Paenibacillus polymyxa]]
-[[Category: Davies, G J]]
+[[Category: Boraston AB]]
-[[Category: Jamal, S]]
+[[Category: Davies GJ]]
-[[Category: Carbohydrate binding]]
+[[Category: Jamal S]]
-[[Category: Carbohydrate-binding module]]
-[[Category: Cbm36]]
-[[Category: Hydrolase]]
-[[Category: Xylan]]
-[[Category: Xylanase]]

1w0n

From Proteopedia

Current revision

Structure of uncomplexed Carbohydrate Binding Domain CBM36

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox