6uxi - Revision history

OCA at 08:00, 11 October 2023

OCA — Wed, 11 Oct 2023 08:00:18 GMT

←Older revision		Revision as of 08:00, 11 October 2023
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	<StructureSection load='6uxi' size='340' side='right'caption='[[6uxi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6uxi' size='340' side='right'caption='[[6uxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uxi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Glycine_hispida~~ Glycine ~~hispida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uxi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UXI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=PLG:N-GLYCINE-~~[~~3-HYDROXY-~~2~~-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SHMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3847 Glycine hispida])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number~~ [~~http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~2~~.1.2.1 2.1.2.1~~] </~~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=6uxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxi OCA], [https://pdbe.org/6uxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uxi RCSB], [https://www.ebi.ac.uk/pdbsum/6uxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxi 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=6uxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxi OCA], [~~http~~://pdbe.org/6uxi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uxi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uxi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~K4FZF8_SOYBN K4FZF8_SOYBN]~~] Interconversion of serine and glycine.[RuleBase:RU000585]	+	[https://www.uniprot.org/uniprot/A0A0R0IK90_SOYBN A0A0R0IK90_SOYBN] Interconversion of serine and glycine.[RuleBase:RU000585]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6uxi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6uxi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine hydroxymethyltransferase 3D structures\|Serine hydroxymethyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Glycine ~~hispida]]~~	+	[[Category: Glycine max]]
-	~~[[Category: Glycine hydroxymethyltransferase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Beamer~~, L J~~]]	+	[[Category: Beamer LJ]]
-	[[Category: Korasick~~, D A~~]]	+	[[Category: Korasick DA]]
-	[[Category: Tanner~~, J J]]~~	+	[[Category: Tanner JJ]]
-	~~[[Category: Cytoplasmic enzyme]]~~	+
-	~~[[Category: Folate metabolism]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Nematode infection resistance]]~~	+
-	~~[[Category: Plant protein]]~~	+
-	~~[[Category: Soybean cyst]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:42, 19 February 2020

OCA — Wed, 19 Feb 2020 07:42:24 GMT

←Older revision		Revision as of 07:42, 19 February 2020
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	<StructureSection load='6uxi' size='340' side='right'caption='[[6uxi]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6uxi' size='340' side='right'caption='[[6uxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6uxi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uxi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_hispida Glycine hispida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UXI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SHMT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3847 Glycine hispida])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </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=6uxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxi OCA], [http://pdbe.org/6uxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uxi RCSB], [http://www.ebi.ac.uk/pdbsum/6uxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxi 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=6uxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxi OCA], [http://pdbe.org/6uxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uxi RCSB], [http://www.ebi.ac.uk/pdbsum/6uxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxi ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/K4FZF8_SOYBN K4FZF8_SOYBN]] Interconversion of serine and glycine.[RuleBase:RU000585]		[[http://www.uniprot.org/uniprot/K4FZF8_SOYBN K4FZF8_SOYBN]] Interconversion of serine and glycine.[RuleBase:RU000585]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Management of the agricultural pathogen soybean cyst nematode (SCN) relies on the use of SCN-resistant soybean cultivars, a strategy that has been failing in recent years. An underutilized source of resistance, in the soybean genotype Peking, is linked to two polymorphisms in serine hydroxy-methyltransferase 8 (SHMT8). SHMT is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that converts L-serine and (6S)-tetrahydrofolate (THF) to glycine and 5,10-methylenetetrahydrofolate. Here, we determined five crystal structures of the 1,884-residue SHMT8 tetramers from the SCN-susceptible cultivar (cv.) Essex and the SCN-resistant cv. Forrest (whose resistance is derived from the SHMT8 polymorphisms in Peking) were determined in complex with various ligands at 1.4 - 2.35 A resolutions. We find that the two Forrest-specific polymorphic substitutions (P130R and N358Y) impact the mobility of a loop near the entrance of the THF-binding site. Ligand-binding and kinetic studies indicate severely reduced affinity for folate and dramatically impaired enzyme activity in Forrest SHMT8. These findings imply widespread effects on folate metabolism in soybean cv. Forrest that have implications for combating the widespread increase in virulent SCN.
		+
		+	Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode.,Korasick DA, Kandoth PK, Tanner JJ, Mitchum MG, Beamer LJ J Biol Chem. 2020 Feb 2. pii: RA119.012256. doi: 10.1074/jbc.RA119.012256. PMID:32014996<ref>PMID:32014996</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6uxi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Glycine hispida]]
	[[Category: Glycine hydroxymethyltransferase]]		[[Category: Glycine hydroxymethyltransferase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 04:29, 13 February 2020

OCA — Thu, 13 Feb 2020 04:29:23 GMT

←Older revision		Revision as of 04:29, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6uxi is ~~ON HOLD until Paper Publication~~	+	==Structure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-Glycine==
-		+	<StructureSection load='6uxi' size='340' side='right'caption='[[6uxi]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6uxi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UXI FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </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=6uxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uxi OCA], [http://pdbe.org/6uxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uxi RCSB], [http://www.ebi.ac.uk/pdbsum/6uxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uxi ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/K4FZF8_SOYBN K4FZF8_SOYBN]] Interconversion of serine and glycine.[RuleBase:RU000585]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Glycine hydroxymethyltransferase]]
		+	[[Category: Large Structures]]
		+	[[Category: Beamer, L J]]
		+	[[Category: Korasick, D A]]
		+	[[Category: Tanner, J J]]
		+	[[Category: Cytoplasmic enzyme]]
		+	[[Category: Folate metabolism]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Nematode infection resistance]]
		+	[[Category: Plant protein]]
		+	[[Category: Soybean cyst]]
		+	[[Category: Transferase]]

OCA at 13:54, 20 November 2019

OCA — Wed, 20 Nov 2019 13:54:44 GMT

←Older revision		Revision as of 13:54, 20 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6uxi is ON HOLD	+	The entry 6uxi is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6uxi" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2019 09:41:29 GMT

Protected "6uxi" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:41, 13 November 2019

OCA: New page: '''Unreleased structure''' The entry 6uxi is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Nov 2019 09:41:28 GMT

New page: '''Unreleased structure''' The entry 6uxi is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6uxi is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]