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6qe8

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Current revision

Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe

Structural highlights

6qe8 is a 1 chain structure with sequence from Aspergillus niger. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.79Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYNA_ASPNG Endo-1,4-beta-xylanase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose.

Publication Abstract from PubMed

Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of beta-xylosidases and endo-beta-1,4-xylanases in the secretomes of Aspergillus niger, by the use of chemical probes inspired by the beta-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.

Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes.,Schroder SP, de Boer C, McGregor NGS, Rowland RJ, Moroz O, Blagova E, Reijngoud J, Arentshorst M, Osborn D, Morant MD, Abbate E, Stringer MA, Krogh KBRM, Raich L, Rovira C, Berrin JG, van Wezel GP, Ram AFJ, Florea BI, van der Marel GA, Codee JDC, Wilson KS, Wu L, Davies GJ, Overkleeft HS ACS Cent Sci. 2019 Jun 26;5(6):1067-1078. doi: 10.1021/acscentsci.9b00221. Epub, 2019 May 24. PMID:31263766^[1]

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

References

↑ Schroder SP, de Boer C, McGregor NGS, Rowland RJ, Moroz O, Blagova E, Reijngoud J, Arentshorst M, Osborn D, Morant MD, Abbate E, Stringer MA, Krogh KBRM, Raich L, Rovira C, Berrin JG, van Wezel GP, Ram AFJ, Florea BI, van der Marel GA, Codee JDC, Wilson KS, Wu L, Davies GJ, Overkleeft HS. Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes. ACS Cent Sci. 2019 Jun 26;5(6):1067-1078. doi: 10.1021/acscentsci.9b00221. Epub, 2019 May 24. PMID:31263766 doi:http://dx.doi.org/10.1021/acscentsci.9b00221

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/6qe8"

Categories: Aspergillus niger | Large Structures | Davies GJ | Rowland RJ | Wu L

@@ Line 3: / Line 3: @@
 <StructureSection load='6qe8' size='340' side='right'caption='[[6qe8]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6qe8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QE8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QE8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6qe8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QE8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HZB:(1~{R},3~{S},4~{R},5~{R})-5-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexane-1,2,3,4-tetrol'>HZB</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.79&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HZB:(1~{R},3~{S},4~{R},5~{R})-5-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexane-1,2,3,4-tetrol'>HZB</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6qe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qe8 OCA], [http://pdbe.org/6qe8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qe8 RCSB], [http://www.ebi.ac.uk/pdbsum/6qe8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qe8 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=6qe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qe8 OCA], [https://pdbe.org/6qe8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qe8 RCSB], [https://www.ebi.ac.uk/pdbsum/6qe8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qe8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/XYNA_ASPNG XYNA_ASPNG]] Endo-1,4-beta-xylanase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose.
+[https://www.uniprot.org/uniprot/XYNA_ASPNG XYNA_ASPNG] Endo-1,4-beta-xylanase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Aspergillus niger]]
-[[Category: Endo-1,4-beta-xylanase]]
 [[Category: Large Structures]]
-[[Category: Davies, G J]]
+[[Category: Davies GJ]]
-[[Category: Rowland, R J]]
+[[Category: Rowland RJ]]
-[[Category: Wu, L]]
+[[Category: Wu L]]
-[[Category: Hydrolase]]

6qe8

From Proteopedia

Current revision

Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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