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5la1

From Proteopedia

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Current revision

The mechanism by which arabinoxylanases can recognise highly decorated xylans

Structural highlights

5la1 is a 1 chain structure with sequence from Acetivibrio thermocellus JW20. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A3DHG6_ACET2

Publication Abstract from PubMed

The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular arabinoxylanase, CtXyl5A, was shown previously to specifically target arabinoxylans. However, the mechanism of substrate recognition displayed by the enzyme remains unclear. Here we report the crystal structure of the tetra-modular arabinoxylanase, and the enzyme in complex with ligands. The data showed that the multi-modular protein adopts a rigid structure, which stabilises the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure indicating positional flexibility. The structure of the enzyme in complex with Xylp-1,4-Xylp-1,4-Xylp-[1,3-Araf]-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (-2* subsite) that abuts onto the catalytic centre. The -2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu68, Tyr92 or Asn139, which interact with arabinose and xylose side chains at the -2* subsite abrogate catalytic activity. Distal to the active site the xylan backbone makes limited apolar contacts with the enzyme and the hydroxyls are solvent exposed. This explains why CtXyl5A is capable of hydrolysing xylans that are extensively decorated, and which are recalcitrant to classic endo-xylanase attack.

The mechanism by which arabinoxylanases can recognise highly decorated xylans.,Labourel A, Crouch LI, Bras JL, Jackson A, Rogowski A, Gray J, Yadav MP, Henrissat B, Fontes CM, Gilbert HJ, Najmudin S, Basle A, Cuskin F J Biol Chem. 2016 Aug 16. pii: jbc.M116.743948. PMID:27531750^[1]

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

References

↑ Labourel A, Crouch LI, Bras JL, Jackson A, Rogowski A, Gray J, Yadav MP, Henrissat B, Fontes CM, Gilbert HJ, Najmudin S, Basle A, Cuskin F. The mechanism by which arabinoxylanases can recognise highly decorated xylans. J Biol Chem. 2016 Aug 16. pii: jbc.M116.743948. PMID:27531750 doi:http://dx.doi.org/10.1074/jbc.M116.743948

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5la1"

@@ Line 1: / Line 1: @@
 ==The mechanism by which arabinoxylanases can recognise highly decorated xylans==
-<StructureSection load='5la1' size='340' side='right' caption='[[5la1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='5la1' size='340' side='right'caption='[[5la1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_dsm_4150 Clostridium thermocellum dsm 4150]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5la1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_JW20 Acetivibrio thermocellus JW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LA1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cther_1146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=492476 Clostridium thermocellum DSM 4150])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [http://pdbe.org/5la1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [http://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 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=5la1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5la1 OCA], [https://pdbe.org/5la1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5la1 RCSB], [https://www.ebi.ac.uk/pdbsum/5la1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5la1 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A3DHG6_ACET2 A3DHG6_ACET2]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Clostridium thermocellum dsm 4150]]
+[[Category: Acetivibrio thermocellus JW20]]
-[[Category: Basle, A]]
+[[Category: Large Structures]]
-[[Category: Crouch, L]]
+[[Category: Basle A]]
-[[Category: Cuskin, F]]
+[[Category: Crouch L]]
-[[Category: Gilbert, H]]
+[[Category: Cuskin F]]
-[[Category: Jackson, A]]
+[[Category: Gilbert H]]
-[[Category: Labourel, A]]
+[[Category: Jackson A]]
-[[Category: Rogowski, A]]
+[[Category: Labourel A]]
-[[Category: Arabinoxylanase glycoside hydrolase carbohydrate binding module arabinose clostridium thermocellum cellulosome]]
+[[Category: Rogowski A]]
-[[Category: Hydrolase]]

5la1

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Current revision

The mechanism by which arabinoxylanases can recognise highly decorated xylans

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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