7vc7 - Revision history

OCA at 17:22, 29 November 2023

OCA — Wed, 29 Nov 2023 17:22:57 GMT

←Older revision		Revision as of 17:22, 29 November 2023
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	<StructureSection load='7vc7' size='340' side='right'caption='[[7vc7]], [[Resolution\|resolution]] 3.08Å' scene=''>		<StructureSection load='7vc7' size='340' side='right'caption='[[7vc7]], [[Resolution\|resolution]] 3.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7vc7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VC7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vc7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VC7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 3.08Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7vc6\|7vc6]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7vc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vc7 OCA], [https://pdbe.org/7vc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vc7 RCSB], [https://www.ebi.ac.uk/pdbsum/7vc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vc7 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=7vc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vc7 OCA], [https://pdbe.org/7vc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vc7 RCSB], [https://www.ebi.ac.uk/pdbsum/7vc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vc7 ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7vc7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7vc7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Xylosidase 3D structures\|Xylosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xylan 1,4-beta-xylosidase~~]]	+	[[Category: Phanerodontia chrysosporium]]
-	[[Category: Igarashi, K]]	+	[[Category: Igarashi K]]
-	[[Category: Kojima, K]]	+	[[Category: Kojima K]]
-	[[Category: Sunagawa, N]]	+	[[Category: Sunagawa N]]
-	~~[[Category: Beta-xylosidase]]~~	+
-	~~[[Category: Glycoside hydrolase family 3]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:13, 16 February 2022

OCA — Wed, 16 Feb 2022 11:13:06 GMT

←Older revision		Revision as of 11:13, 16 February 2022
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	==The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)==		==The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)==
-	<StructureSection load='7vc7' size='340' side='right'caption='[[7vc7]]' scene=''>	+	<StructureSection load='7vc7' size='340' side='right'caption='[[7vc7]], [[Resolution\|resolution]] 3.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VC7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vc7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VC7 FirstGlance]. <br>
-	</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=7vc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vc7 OCA], [https://pdbe.org/7vc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vc7 RCSB], [https://www.ebi.ac.uk/pdbsum/7vc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vc7 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7vc6\|7vc6]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7vc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vc7 OCA], [https://pdbe.org/7vc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vc7 RCSB], [https://www.ebi.ac.uk/pdbsum/7vc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vc7 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) beta-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the KM values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X2), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.
		+
		+	Comparison of Glycoside Hydrolase family 3 beta-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems.,Kojima K, Sunagawa N, Mikkelsen NE, Hansson H, Karkehabadi S, Samejima M, Sandgren M, Igarashi K J Biol Chem. 2022 Feb 1:101670. doi: 10.1016/j.jbc.2022.101670. PMID:35120929<ref>PMID:35120929</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vc7" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Igarashi K]]	+	[[Category: Xylan 1,4-beta-xylosidase]]
-	[[Category: Kojima K]]	+	[[Category: Igarashi, K]]
-	[[Category: Sunagawa N]]	+	[[Category: Kojima, K]]
		+	[[Category: Sunagawa, N]]
		+	[[Category: Beta-xylosidase]]
		+	[[Category: Glycoside hydrolase family 3]]
		+	[[Category: Hydrolase]]

OCA at 07:27, 9 February 2022

OCA — Wed, 09 Feb 2022 07:27:11 GMT

←Older revision		Revision as of 07:27, 9 February 2022
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-	'''Unreleased structure'''

-	The ~~entry~~ 7vc7 ~~is ON HOLD until Paper Publication~~	+	==The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)==
-		+	<StructureSection load='7vc7' size='340' side='right'caption='[[7vc7]]' scene=''>
-	~~Authors~~: ~~Kojima~~, K., ~~Sunagawa~~, N., ~~Igarashi~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VC7 FirstGlance]. <br>
-	~~Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)~~	+	</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=7vc7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vc7 OCA], [https://pdbe.org/7vc7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vc7 RCSB], [https://www.ebi.ac.uk/pdbsum/7vc7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vc7 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Igarashi, K]]	+	__TOC__
-	[[Category: Kojima, K]]	+	</StructureSection>
-	[[Category: Sunagawa, N]]	+	[[Category: Large Structures]]
		+	[[Category: Igarashi K]]
		+	[[Category: Kojima K]]
		+	[[Category: Sunagawa N]]

OCA at 12:48, 27 October 2021

OCA — Wed, 27 Oct 2021 12:48:32 GMT

←Older revision		Revision as of 12:48, 27 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vc7 is ON HOLD	+	The entry 7vc7 is ON HOLD until Paper Publication

	Authors: Kojima, K., Sunagawa, N., Igarashi, K.		Authors: Kojima, K., Sunagawa, N., Igarashi, K.

OCA at 08:25, 15 September 2021

OCA — Wed, 15 Sep 2021 08:25:45 GMT

←Older revision		Revision as of 08:25, 15 September 2021
Line 3:		Line 3:
	The entry 7vc7 is ON HOLD		The entry 7vc7 is ON HOLD

-	Authors: ~~Keisuke~~, K., ~~Naoki~~, S., ~~Kiyohiko~~, I.	+	Authors: Kojima, K., Sunagawa, N., Igarashi, K.

	Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)		Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Naoki~~, S]]	+	[[Category: Igarashi, K]]
-	[[Category: ~~Kiyohiko~~, I]]	+	[[Category: Kojima, K]]
-	[[Category: ~~Keisuke~~, K]]	+	[[Category: Sunagawa, N]]

OCA: Protected "7vc7" [edit=sysop:move=sysop]

OCA — Wed, 08 Sep 2021 08:04:32 GMT

Protected "7vc7" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:04, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7vc7 is ON HOLD Authors: Keisuke, K., Naoki, S., Kiyohiko, I. Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3...

OCA — Wed, 08 Sep 2021 08:04:31 GMT

New page: '''Unreleased structure''' The entry 7vc7 is ON HOLD Authors: Keisuke, K., Naoki, S., Kiyohiko, I. Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3...

New page

'''Unreleased structure'''

The entry 7vc7 is ON HOLD

Authors: Keisuke, K., Naoki, S., Kiyohiko, I.

Description: The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3)
[[Category: Unreleased Structures]]
[[Category: Naoki, S]]
[[Category: Kiyohiko, I]]
[[Category: Keisuke, K]]