7dfn - Revision history

OCA at 16:32, 29 November 2023

OCA — Wed, 29 Nov 2023 16:32:20 GMT

←Older revision		Revision as of 16:32, 29 November 2023
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	==Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose==		==Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose==
-	<StructureSection load='7dfn' size='340' side='right'caption='[[7dfn]]' scene=''>	+	<StructureSection load='7dfn' size='340' side='right'caption='[[7dfn]], [[Resolution\|resolution]] 2.00Å' 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=7DFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dfn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivaceoviridis Streptomyces olivaceoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFN 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=7dfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfn OCA], [https://pdbe.org/7dfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dfn RCSB], [https://www.ebi.ac.uk/pdbsum/7dfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfn ProSAT]</span></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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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'>[https://proteopedia.org/fgij/fg.htm?mol=7dfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfn OCA], [https://pdbe.org/7dfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dfn RCSB], [https://www.ebi.ac.uk/pdbsum/7dfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A7G1MBT0_STROI A0A7G1MBT0_STROI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the - side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite - 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-beta-D-xylopyranosyl-(1-->4)-[O-alpha-L-arabinofuranosyl-(1-->3)]-O-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranose (Ara(3)Xyl(4)) and O-beta-D-xylopyranosyl-(1-->4)-[O-4-O-methyl-alpha-D-glucuronopyranosyl-(l-->2)]-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranose (MeGlcA(3)Xyl(4)) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a beta-jerryroll fold structure, and the catalytic cleft is located on the inner beta-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and - 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides. KEY POINTS: * Crystal structure of family 11 beta-xylanase from Streptomyces olivaceoviridis was determined. * Topology of substrate-binding cleft of family 11 beta-xylanase from Streptomyces olivaceoviridis was characterized. * Mode of action of family 11 beta-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated.
		+
		+	Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.,Fujimoto Z, Kishine N, Teramoto K, Tsutsui S, Kaneko S Appl Microbiol Biotechnol. 2021 Mar;105(5):1943-1952. doi: , 10.1007/s00253-021-11098-0. Epub 2021 Feb 10. PMID:33564921<ref>PMID:33564921</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dfn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Streptomyces olivaceoviridis]]
	[[Category: Fujimoto Z]]		[[Category: Fujimoto Z]]
	[[Category: Kaneko S]]		[[Category: Kaneko S]]
	[[Category: Kishine N]]		[[Category: Kishine N]]

OCA at 18:04, 10 March 2021

OCA — Wed, 10 Mar 2021 18:04:54 GMT

←Older revision		Revision as of 18:04, 10 March 2021
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	<StructureSection load='7dfn' size='340' side='right'caption='[[7dfn]]' scene=''>		<StructureSection load='7dfn' size='340' side='right'caption='[[7dfn]]' 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=7DFN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7DFN FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFN FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7dfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfn OCA], [~~http~~://pdbe.org/7dfn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7dfn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7dfn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfn ProSAT]</span></td></tr>	+	</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=7dfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfn OCA], [https://pdbe.org/7dfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dfn RCSB], [https://www.ebi.ac.uk/pdbsum/7dfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfn ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 06:49, 30 December 2020

OCA — Wed, 30 Dec 2020 06:49:02 GMT

←Older revision		Revision as of 06:49, 30 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7dfn is ON HOLD~~	+	==Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose==
-		+	<StructureSection load='7dfn' size='340' side='right'caption='[[7dfn]]' scene=''>
-	~~Authors: Fujimoto, Z., Kishine, N., Kaneko, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DFN FirstGlance]. <br>
-	~~Description:~~ Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7dfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfn OCA], [http://pdbe.org/7dfn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dfn RCSB], [http://www.ebi.ac.uk/pdbsum/7dfn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfn ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Kishine~~, N]]	+	__TOC__
-	[[Category: Fujimoto, Z]]	+	</StructureSection>
-	[[Category: Kaneko, S]]	+	[[Category: Large Structures]]
		+	[[Category: Fujimoto Z]]
		+	[[Category: Kaneko S]]
		+	[[Category: Kishine N]]

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

OCA — Wed, 18 Nov 2020 08:02:09 GMT

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

←Older revision

Revision as of 08:02, 18 November 2020

OCA: New page: '''Unreleased structure''' The entry 7dfn is ON HOLD Authors: Fujimoto, Z., Kishine, N., Kaneko, S. Description: Crystal structure of glycoside hydrolase family 11 beta-xylanase from S...

OCA — Wed, 18 Nov 2020 08:02:08 GMT

New page: '''Unreleased structure''' The entry 7dfn is ON HOLD Authors: Fujimoto, Z., Kishine, N., Kaneko, S. Description: Crystal structure of glycoside hydrolase family 11 beta-xylanase from S...

New page

'''Unreleased structure'''

The entry 7dfn is ON HOLD

Authors: Fujimoto, Z., Kishine, N., Kaneko, S.

Description: Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose
[[Category: Unreleased Structures]]
[[Category: Kishine, N]]
[[Category: Fujimoto, Z]]
[[Category: Kaneko, S]]