5bum - Revision history

OCA at 16:05, 8 November 2023

OCA — Wed, 08 Nov 2023 16:05:19 GMT

←Older revision		Revision as of 16:05, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='5bum' size='340' side='right'caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5bum' size='340' side='right'caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Common_horsetail Common horsetail~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BUM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equisetum_arvense Equisetum arvense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BUM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[4pxv\|4pxv]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">eachiA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3258 Common horsetail])~~</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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [https://pdbe.org/5bum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [https://www.ebi.ac.uk/pdbsum/5bum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bum 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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [https://pdbe.org/5bum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [https://www.ebi.ac.uk/pdbsum/5bum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bum ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C7G3I3_EQUAR C7G3I3_EQUAR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Common horsetail~~]]	+	[[Category: Equisetum arvense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukamizo, T]]	+	[[Category: Fukamizo T]]
-	[[Category: Kitaoku, Y]]	+	[[Category: Kitaoku Y]]
-	[[Category: Numata, T]]	+	[[Category: Numata T]]
-	[[Category: Ohnuma, T]]	+	[[Category: Ohnuma T]]
-	[[Category: Taira, T]]	+	[[Category: Taira T]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Carbohydrate-binding module]]~~	+
-	~~[[Category: Chitinase]]~~	+
-	~~[[Category: Lysm domain]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 09:49, 22 June 2022

OCA — Wed, 22 Jun 2022 09:49:38 GMT

←Older revision		Revision as of 09:49, 22 June 2022
Line 3:		Line 3:
	<StructureSection load='5bum' size='340' side='right'caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5bum' size='340' side='right'caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Common_horsetail Common horsetail]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BUM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Common_horsetail Common horsetail]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BUM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxv\|4pxv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4pxv\|4pxv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eachiA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3258 Common horsetail])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eachiA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3258 Common horsetail])</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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [~~http~~://pdbe.org/5bum PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bum PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bum 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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [https://pdbe.org/5bum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [https://www.ebi.ac.uk/pdbsum/5bum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bum ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414-423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but in fungi. Here, we produced a similar GH18 chitinase with one N-terminal LysM module (EaLysM) from the fern, Equisetum arvense (EaChiA, Inamine et al., Biosci. Biotechnol. Biochem., 79, 1296-1304, 2015), using an Escherichia coli expression system and characterized for its structure and mechanism of action. The crystal structure of EaLysM exhibited an almost identical fold (betaalphaalphabeta) to that of PrLysM2. From isothermal titration calorimetry and nuclear magnetic resonance, the binding mode and affinities of EaLysM for chitooligosaccharides (GlcNAc)n (3, 4, 5, and 6) were found to be comparable to those of PrLysM2. The LysM module in EaChiA is likely to bind (GlcNAc)n almost independently through CH-pi stacking of a Tyr residue with the pyranose ring. The (GlcNAc)n-binding mode of LysMs in the LysM-chitinase conjugates from fern plants appears to differ from that of plant LysMs acting in chitin- or Nod-signal perception, in which multiple LysMs cooperatively act on (GlcNAc)n. Phylogenetic analysis suggested that LysM-GH18 conjugates of fern plants formed a monophyletic group and had been separated earlier than forming the clade of fungal chitinases with LysMs.
		+
		+	Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants.,Kitaoku Y, Taira T, Numata T, Ohnuma T, Fukamizo T Plant Sci. 2022 Aug;321:111310. doi: 10.1016/j.plantsci.2022.111310. Epub 2022, May 6. PMID:35696910<ref>PMID:35696910</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5bum" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Chitinase 3D structures\|Chitinase 3D structures]]		*[[Chitinase 3D structures\|Chitinase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:08, 19 February 2020

OCA — Wed, 19 Feb 2020 07:08:17 GMT

←Older revision		Revision as of 07:08, 19 February 2020
Line 1:		Line 1:

	==Crystal Structure of LysM domain from Equisetum arvense chitinase A==		==Crystal Structure of LysM domain from Equisetum arvense chitinase A==
-	<StructureSection load='5bum' size='340' side='right' caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5bum' size='340' side='right'caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BUM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Common_horsetail Common horsetail]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BUM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxv\|4pxv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxv\|4pxv]]</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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [http://pdbe.org/5bum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [http://www.ebi.ac.uk/pdbsum/5bum PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">eachiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3258 Common horsetail])</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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [http://pdbe.org/5bum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [http://www.ebi.ac.uk/pdbsum/5bum PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bum ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Chitinase 3D structures\|Chitinase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Common horsetail]]
		+	[[Category: Large Structures]]
	[[Category: Fukamizo, T]]		[[Category: Fukamizo, T]]
	[[Category: Kitaoku, Y]]		[[Category: Kitaoku, Y]]

OCA at 15:20, 20 June 2016

OCA — Mon, 20 Jun 2016 15:20:10 GMT

←Older revision		Revision as of 15:20, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5bum ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of LysM domain from Equisetum arvense chitinase A==
-		+	<StructureSection load='5bum' size='340' side='right' caption='[[5bum]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~: ~~Kitaoku, Y~~.~~, Numata, T~~.~~, Ohnuma, T~~.~~, Taira, T~~.~~, Fukamizo, T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5bum]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BUM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BUM FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of LysM domain from Equisetum arvense chitinase A~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4pxv\|4pxv]]</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=5bum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bum OCA], [http://pdbe.org/5bum PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bum RCSB], [http://www.ebi.ac.uk/pdbsum/5bum PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fukamizo, T]]		[[Category: Fukamizo, T]]
		+	[[Category: Kitaoku, Y]]
	[[Category: Numata, T]]		[[Category: Numata, T]]
		+	[[Category: Ohnuma, T]]
	[[Category: Taira, T]]		[[Category: Taira, T]]
-	[[Category: ~~Kitaoku, Y~~]]	+	[[Category: Carbohydrate]]
-	[[Category: ~~Ohnuma, T~~]]	+	[[Category: Carbohydrate-binding module]]
		+	[[Category: Chitinase]]
		+	[[Category: Lysm domain]]
		+	[[Category: Sugar binding protein]]

OCA at 11:41, 24 June 2015

OCA — Wed, 24 Jun 2015 11:41:47 GMT

←Older revision		Revision as of 11:41, 24 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5bum is ON HOLD	+	The entry 5bum is ON HOLD until Paper Publication

	Authors: Kitaoku, Y., Numata, T., Ohnuma, T., Taira, T., Fukamizo, T.		Authors: Kitaoku, Y., Numata, T., Ohnuma, T., Taira, T., Fukamizo, T.

OCA at 13:54, 17 June 2015

OCA — Wed, 17 Jun 2015 13:54:54 GMT

←Older revision		Revision as of 13:54, 17 June 2015
Line 3:		Line 3:
	The entry 5bum is ON HOLD		The entry 5bum is ON HOLD

-	Authors: Kitaoku Y., Numata T., Ohnuma T., Taira T., Fukamizo T.	+	Authors: Kitaoku, Y., Numata, T., Ohnuma, T., Taira, T., Fukamizo, T.

	Description: Crystal Structure of LysM domain from Equisetum arvense chitinase A		Description: Crystal Structure of LysM domain from Equisetum arvense chitinase A
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Taira~~ T]]	+	[[Category: Fukamizo, T]]
-	[[Category: Numata T]]	+	[[Category: Numata, T]]
-	[[Category: ~~Ohnuma~~ T]]	+	[[Category: Taira, T]]
-	[[Category: ~~Fukamizo T~~]]	+	[[Category: Kitaoku, Y]]
-	[[Category: ~~Kitaoku Y~~]]	+	[[Category: Ohnuma, T]]

OCA: Protected "5bum" [edit=sysop:move=sysop]

OCA — Wed, 10 Jun 2015 13:05:27 GMT

Protected "5bum" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:05, 10 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bum is ON HOLD Authors: Kitaoku Y., Numata T., Ohnuma T., Taira T., Fukamizo T. Description: Crystal Structure of LysM domain from Equisetum arven...

OCA — Wed, 10 Jun 2015 13:05:26 GMT

New page: '''Unreleased structure''' The entry 5bum is ON HOLD Authors: Kitaoku Y., Numata T., Ohnuma T., Taira T., Fukamizo T. Description: Crystal Structure of LysM domain from Equisetum arven...

New page

'''Unreleased structure'''

The entry 5bum is ON HOLD

Authors: Kitaoku Y., Numata T., Ohnuma T., Taira T., Fukamizo T.

Description: Crystal Structure of LysM domain from Equisetum arvense chitinase A
[[Category: Unreleased Structures]]
[[Category: Taira T]]
[[Category: Numata T]]
[[Category: Ohnuma T]]
[[Category: Fukamizo T]]
[[Category: Kitaoku Y]]