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6q7i

From Proteopedia

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GH3 exo-beta-xylosidase (XlnD)

Structural highlights

6q7i is a 2 chain structure with sequence from Aspergillus nidulans FGSC A4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.48Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYND_EMENI Xylan 1,4-beta-xylosidase 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.^[1] ^[2]

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^[3]

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

References

↑ Bauer S, Vasu P, Persson S, Mort AJ, Somerville CR. Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls. Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11417-22. Epub 2006 Jul 14. PMID:16844780 doi:http://dx.doi.org/0604632103
↑ Perez-Gonzalez JA, van Peij NN, Bezoen A, MacCabe AP, Ramon D, de Graaff LH. Molecular cloning and transcriptional regulation of the Aspergillus nidulans xlnD gene encoding a beta-xylosidase. Appl Environ Microbiol. 1998 Apr;64(4):1412-9. PMID:9546179
↑ 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 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6q7i"

@@ Line 3: / Line 3: @@
 <StructureSection load='6q7i' size='340' side='right'caption='[[6q7i]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6q7i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q7I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q7I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6q7i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans_FGSC_A4 Aspergillus nidulans FGSC A4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q7I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.48&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6q7j|6q7j]]</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=6q7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q7i OCA], [https://pdbe.org/6q7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q7i RCSB], [https://www.ebi.ac.uk/pdbsum/6q7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q7i ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xlnD, xylA, AN2359 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227321 Aspergillus nidulans])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></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=6q7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q7i OCA], [http://pdbe.org/6q7i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q7i RCSB], [http://www.ebi.ac.uk/pdbsum/6q7i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q7i ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/XYND_EMENI XYND_EMENI]] Xylan 1,4-beta-xylosidase 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.<ref>PMID:16844780</ref> <ref>PMID:9546179</ref>
+[https://www.uniprot.org/uniprot/XYND_EMENI XYND_EMENI] Xylan 1,4-beta-xylosidase 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.<ref>PMID:16844780</ref> <ref>PMID:9546179</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 19: @@
 </div>
 <div class="pdbe-citations 6q7i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Xylosidase 3D structures|Xylosidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aspergillus nidulans]]
+[[Category: Aspergillus nidulans FGSC A4]]
 [[Category: Large Structures]]
-[[Category: Xylan 1,4-beta-xylosidase]]
+[[Category: Blagova E]]
-[[Category: Blagova, E]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Moroz O]]
-[[Category: Moroz, O]]
+[[Category: Rowland RJ]]
-[[Category: Rowland, R J]]
+[[Category: Wu L]]
-[[Category: Wu, L]]
-[[Category: Hydrolase]]

6q7i

From Proteopedia

Current revision

GH3 exo-beta-xylosidase (XlnD)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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