4xre - Revision history

OCA at 15:30, 8 November 2023

2023-11-08T15:30:41Z

←Older revision		Revision as of 15:30, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ginkgo_biloba Ginkgo biloba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ginkgo_biloba Ginkgo biloba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.597Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [https://pdbe.org/4xre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [https://www.ebi.ac.uk/pdbsum/4xre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre 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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [https://pdbe.org/4xre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [https://www.ebi.ac.uk/pdbsum/4xre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:48, 26 April 2023

2023-04-26T17:48:33Z

←Older revision		Revision as of 17:48, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xre' size='340' side='right'caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4xre' size='340' side='right'caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ginbi Ginbi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XRE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ginkgo_biloba Ginkgo biloba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XRE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [https://pdbe.org/4xre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [https://www.ebi.ac.uk/pdbsum/4xre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GNK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3311 GINBI])~~</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [~~http~~://pdbe.org/4xre PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xre PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GNK2_GINBI GNK2_GINBI]] Possesses antifungal activity against F.oxysporum, T.reesei and C.albicans. Weakly inhibits the aspartic acid protease pepsin activity.<ref>PMID:17338634</ref>	+	[https://www.uniprot.org/uniprot/GNK2_GINBI GNK2_GINBI] Possesses antifungal activity against F.oxysporum, T.reesei and C.albicans. Weakly inhibits the aspartic acid protease pepsin activity.<ref>PMID:17338634</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ginbi~~]]	+	[[Category: Ginkgo biloba]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hatano, K]]	+	[[Category: Hatano K]]
-	[[Category: Miyakawa, T]]	+	[[Category: Miyakawa T]]
-	[[Category: Miyauchi, Y]]	+	[[Category: Miyauchi Y]]
-	[[Category: Sawano, Y]]	+	[[Category: Sawano Y]]
-	[[Category: Suwa, Y]]	+	[[Category: Suwa Y]]
-	[[Category: Tanokura, M]]	+	[[Category: Tanokura M]]
-	~~[[Category: Antifungal activity]]~~	+
-	~~[[Category: Antifungal protein]]~~	+
-	~~[[Category: C-x8-c-x2-c motif]]~~	+
-	~~[[Category: Lectin~~]]	+

OCA at 23:39, 5 June 2019

2019-06-05T23:39:09Z

←Older revision		Revision as of 23:39, 5 June 2019
Line 1:		Line 1:

	==Crystal structure of Gnk2 complexed with mannose==		==Crystal structure of Gnk2 complexed with mannose==
-	<StructureSection load='4xre' size='340' side='right' caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='4xre' size='340' side='right'caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ginbi Ginbi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GNK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3311 GINBI])</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [http://pdbe.org/4xre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [http://www.ebi.ac.uk/pdbsum/4xre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [http://pdbe.org/4xre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [http://www.ebi.ac.uk/pdbsum/4xre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ginbi]]
		+	[[Category: Large Structures]]
	[[Category: Hatano, K]]		[[Category: Hatano, K]]
	[[Category: Miyakawa, T]]		[[Category: Miyakawa, T]]

OCA at 18:44, 1 February 2017

2017-02-01T18:44:43Z

←Older revision		Revision as of 18:44, 1 February 2017
Line 1:		Line 1:
		+
	==Crystal structure of Gnk2 complexed with mannose==		==Crystal structure of Gnk2 complexed with mannose==
	<StructureSection load='4xre' size='340' side='right' caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='4xre' size='340' side='right' caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [http://www.ebi.ac.uk/pdbsum/4xre PDBsum]</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [http://pdbe.org/4xre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [http://www.ebi.ac.uk/pdbsum/4xre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xre ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4xre" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:53, 25 February 2015

2015-02-25T13:53:44Z

←Older revision		Revision as of 13:53, 25 February 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Gnk2 complexed with mannose==
		+	<StructureSection load='4xre' size='340' side='right' caption='[[4xre]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xre]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XRE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a2e\|3a2e]]</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=4xre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xre OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xre RCSB], [http://www.ebi.ac.uk/pdbsum/4xre PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GNK2_GINBI GNK2_GINBI]] Possesses antifungal activity against F.oxysporum, T.reesei and C.albicans. Weakly inhibits the aspartic acid protease pepsin activity.<ref>PMID:17338634</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plants have a variety of mechanisms for defending against plant pathogens and tolerating environmental stresses such as drought and high salinity. Ginkbilobin2 (Gnk2) is a seed storage protein in gymnosperm that possesses antifungal activity and a plant-specific cysteine-rich motif (domain of unknown function26 [DUF26]). The Gnk2-homologous sequence is also observed in an extracellular region of cysteine-rich repeat receptor-like kinases that function in response to biotic and abiotic stresses. Here, we report the lectin-like molecular function of Gnk2 and the structural basis of its monosaccharide recognition. Nuclear magnetic resonance experiments showed that mannan was the only yeast (Saccharomyces cerevisiae) cell wall polysaccharide that interacted with Gnk2. Gnk2 also interacted with mannose, a building block of mannan, with a specificity that was similar to those of mannose-binding legume lectins, by strictly recognizing the configuration of the hydroxy group at the C4 position of the monosaccharide. The crystal structure of Gnk2 in complex with mannose revealed that three residues (asparagine-11, arginine-93, and glutamate-104) recognized mannose by hydrogen bonds, which defined the carbohydrate-binding specificity. These interactions were directly related to the ability of Gnk2 to inhibit the growth of fungi, including the plant pathogenic Fusarium spp., which were disrupted by mutation of arginine-93 or the presence of yeast mannan in the assay system. In addition, Gnk2 did not inhibit the growth of a yeast mutant strain lacking the alpha1,2-linked mannose moiety. These results provide insights into the molecular basis of the DUF26 protein family.

-	~~The entry 4xre is ON HOLD~~	+	A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity.,Miyakawa T, Hatano K, Miyauchi Y, Suwa Y, Sawano Y, Tanokura M Plant Physiol. 2014 Oct;166(2):766-78. doi: 10.1104/pp.114.242636. Epub 2014 Aug , 19. PMID:25139159<ref>PMID:25139159</ref>

-	~~Authors: Miyakawa~~, T.~~, Hatano, K~~.~~, Miyauchi, Y., Suwa, Y., Sawano, Y., Tanokura, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of Gnk2 complexed with mannose~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hatano, K]]
		+	[[Category: Miyakawa, T]]
		+	[[Category: Miyauchi, Y]]
	[[Category: Sawano, Y]]		[[Category: Sawano, Y]]
-	[[Category: Hatano, K]]
	[[Category: Suwa, Y]]		[[Category: Suwa, Y]]
-	[[Category: Miyauchi, Y]]
	[[Category: Tanokura, M]]		[[Category: Tanokura, M]]
-	[[Category: ~~Miyakawa, T~~]]	+	[[Category: Antifungal activity]]
		+	[[Category: Antifungal protein]]
		+	[[Category: C-x8-c-x2-c motif]]
		+	[[Category: Lectin]]

OCA: Protected "4xre" [edit=sysop:move=sysop]

2015-01-28T15:44:25Z

Protected "4xre" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:44, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xre is ON HOLD Authors: Miyakawa, T., Hatano, K., Miyauchi, Y., Suwa, Y., Sawano, Y., Tanokura, M. Description: Crystal structure of Gnk2 complexe...

2015-01-28T15:44:24Z

New page: '''Unreleased structure''' The entry 4xre is ON HOLD Authors: Miyakawa, T., Hatano, K., Miyauchi, Y., Suwa, Y., Sawano, Y., Tanokura, M. Description: Crystal structure of Gnk2 complexe...

New page

'''Unreleased structure'''

The entry 4xre is ON HOLD

Authors: Miyakawa, T., Hatano, K., Miyauchi, Y., Suwa, Y., Sawano, Y., Tanokura, M.

Description: Crystal structure of Gnk2 complexed with mannose
[[Category: Unreleased Structures]]
[[Category: Sawano, Y]]
[[Category: Hatano, K]]
[[Category: Suwa, Y]]
[[Category: Miyauchi, Y]]
[[Category: Tanokura, M]]
[[Category: Miyakawa, T]]