Sandbox1503 - Revision history

Loïc Plessis at 20:07, 11 January 2019

2019-01-11T20:07:14Z

←Older revision		Revision as of 20:07, 11 January 2019
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	</StructureSection>		</StructureSection>
	== References ==		== References ==
-	~~<references/>~~	+
-	~~__TOC__~~	+	(1) Momma M, Fujimoto Z. Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis. Biosci Biotechnol Biochem. 2012 Aug 7. PMID:22878205
-	~~</StructureSection>~~	+
	[[Category: Japanese rice]]		[[Category: Japanese rice]]
	[[Category: NDP-glucose--starch glucosyltransferase]]		[[Category: NDP-glucose--starch glucosyltransferase]]

Loïc Plessis at 20:03, 11 January 2019

2019-01-11T20:03:03Z

←Older revision		Revision as of 20:03, 11 January 2019
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	[[Image:Catalytic activity 3vuf'.jpg\|900px\|]]		[[Image:Catalytic activity 3vuf'.jpg\|900px\|]]

-	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.	+	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.


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	[[Image:oui.jpg\|900px\|]]		[[Image:oui.jpg\|900px\|]]
		+
		+	==Relevance==
		+
		+	Amylose synthesis allows to the plant having some provisions, for a future seed or for some organ for passing bad seasons. In the rice, it is for a future seed, which is the rice itself. In this forme, amylose is chemically stable. This means that it can’t react except by depolymerisation or polymerisation, but not for producing bioenergy, like ATP or any others. Another property of this form of glucose, is that it doesn’t modify the chemical potential of the cell, which is very good and doesn’t unsettle the equilibrium of the cell.

	== Disease ==		== Disease ==

Loïc Plessis at 19:52, 11 January 2019

2019-01-11T19:52:05Z

←Older revision		Revision as of 19:52, 11 January 2019
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	'''Secondary structure:'''		'''Secondary structure:'''
		+
	[[Image:oui.jpg\|900px\|]]		[[Image:oui.jpg\|900px\|]]

Loïc Plessis at 19:51, 11 January 2019

2019-01-11T19:51:39Z

←Older revision		Revision as of 19:51, 11 January 2019
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-	=3vuf ~~Protein(title here)~~=	+	=3vuf=
	<StructureSection load='3vuf' size='340' side='right' caption='[[3vuf]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3vuf' size='340' side='right' caption='[[3vuf]], [[Resolution\|resolution]] 3.00Å' scene=''>
	3vuf is a 1 chain structure protein which is synthesized by the Japanese rice (Oryza sativa japonica). it’s an enzyme, more accurately a transferase. It’s a NDP-glucose--starch glucosyltransferase, which is involved in the synthesis of amylose in the rice. This enzyme is located chloroplast and in amyloplast.		3vuf is a 1 chain structure protein which is synthesized by the Japanese rice (Oryza sativa japonica). it’s an enzyme, more accurately a transferase. It’s a NDP-glucose--starch glucosyltransferase, which is involved in the synthesis of amylose in the rice. This enzyme is located chloroplast and in amyloplast.

Loïc Plessis at 19:49, 11 January 2019

2019-01-11T19:49:58Z

←Older revision		Revision as of 19:49, 11 January 2019
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

-	== ~~Disease~~ ==	+	== Structural highlights ==
-	~~The~~ protein ~~3vuf has '''allergenic properties'''~~, ~~for example in mammals it~~ can bind to ~~Immunoglobulin E (IgE) causing~~ an ~~allergic response~~.	+	This protein is an enzyme, which is formed from one monomer and can bind to ADP. It binds to the ADP-glucose with amino acids 97,100, 408, 413,462 and 492. This allow the formation of an hydrophobic pocket in which ADP-glucose can binds to and in which he is protected from water and hydrolyse. we can also see that 3vuf can binds sulfate. This hydrophobic cage is allowed by the beta sheets and alpha helices that the protein have.

		+	<table><tr><td colspan='2'>[[3vuf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VUF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <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">[[3vue\|3vue]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NDP-glucose--starch_glucosyltransferase NDP-glucose--starch glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.242 2.4.1.242] </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=3vuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vuf OCA], [http://pdbe.org/3vuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vuf RCSB], [http://www.ebi.ac.uk/pdbsum/3vuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vuf ProSAT]</span></td></tr>
		+	</table>
		+	This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

	== Structure ==		== Structure ==
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	[[Image:oui.jpg\|900px\|]]		[[Image:oui.jpg\|900px\|]]

-	== ~~Structural highlights~~ ==	+	== Disease ==
-	~~This~~ protein is an enzyme, which is formed from one monomer and can bind to ADP. It binds to the ADP-glucose with amino acids 97,100, 408, 413,462 and 492. This allow the formation of an hydrophobic pocket in which ADP-glucose can binds to and in which he is protected from water and hydrolyse. we can also see that 3vuf ~~can binds sulfate. This hydrophobic cage is allowed by the beta sheets and alpha helices that the protein have.~~	+	The protein 3vuf has '''allergenic properties''', for example in mammals it can bind to Immunoglobulin E (IgE) causing an allergic response.
-		+
-	~~<table><tr><td colspan=~~'2'>[[3vuf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VUF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VUF FirstGlance]. <br>	+
-	~~</td></tr><tr id=~~'~~ligand~~'~~><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name=~~'~~pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE~~'~~>ADP</scene>~~, ~~<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">[[3vue\|3vue]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice]~~)~~</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NDP-glucose--starch_glucosyltransferase NDP-glucose--starch glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.242 2.4.1.242] </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=3vuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vuf OCA], [http://pdbe.org/3vuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vuf RCSB], [http://www.ebi.ac.uk/pdbsum/3vuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vuf ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.	+

	</StructureSection>		</StructureSection>

Loïc Plessis at 19:45, 11 January 2019

2019-01-11T19:45:36Z

←Older revision		Revision as of 19:45, 11 January 2019
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	[[http://www.uniprot.org/uniprot/SSG1_ORYSJ SSG1_ORYSJ]] Required for the synthesis of amylose in endosperm.[HAMAP-Rule:MF_00484]		[[http://www.uniprot.org/uniprot/SSG1_ORYSJ SSG1_ORYSJ]] Required for the synthesis of amylose in endosperm.[HAMAP-Rule:MF_00484]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The catalytic domain of rice (Oryza sativa japonica) granule bound starch synthase I (OsGBSSI-CD) was overexpressed and the three-dimensional structures of the ligand-free and ADP-bound forms were determined. The structures were similar to those reported for bacterial and archaeal glycogen synthases, which belong to glycosyltransferase family 5. They had Rossmann fold N- and C-domains connected by canonical two-hinge peptides, and an interdomain disulfide bond that appears to be conserved in the Poaceae plant family. The presence of three covalent linkages might explain why both OsGBSSI-CD structures adopted only the closed domain arrangement.
-
-	Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis.,Momma M, Fujimoto Z Biosci Biotechnol Biochem. 2012 Aug 7. PMID:22878205<ref>PMID:22878205</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3vuf" style="background-color:#fffaf0;"></div>

	== Disease ==		== Disease ==
	The protein 3vuf has '''allergenic properties''', for example in mammals it can bind to Immunoglobulin E (IgE) causing an allergic response.		The protein 3vuf has '''allergenic properties''', for example in mammals it can bind to Immunoglobulin E (IgE) causing an allergic response.

-	== Relevance ==

	== Structure ==		== Structure ==
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	LAKENVAAP		LAKENVAAP
-

Loïc Plessis at 19:44, 11 January 2019

2019-01-11T19:44:36Z

←Older revision		Revision as of 19:44, 11 January 2019
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	== Function ==		== Function ==
	The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :		The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :
-	[[Image:Catalytic activity 3vuf'\|900px\|~~.jpg~~]]	+	[[Image:Catalytic activity 3vuf'.jpg\|900px\|]]

	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.		This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.

Loïc Plessis at 19:43, 11 January 2019

2019-01-11T19:43:34Z

←Older revision		Revision as of 19:43, 11 January 2019
Line 6:		Line 6:
	== Function ==		== Function ==
	The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :		The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :
-	[[Image:Catalytic activity 3vuf'.jpg]]	+	[[Image:Catalytic activity 3vuf'\|900px\|.jpg]]

	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.		This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.

Loïc Plessis at 19:42, 11 January 2019

2019-01-11T19:42:55Z

←Older revision		Revision as of 19:42, 11 January 2019
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	[[Image:Catalytic activity 3vuf'.jpg]]		[[Image:Catalytic activity 3vuf'.jpg]]

-	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.	+	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.

Loïc Plessis at 19:41, 11 January 2019

2019-01-11T19:41:38Z

←Older revision		Revision as of 19:41, 11 January 2019
Line 6:		Line 6:
	== Function ==		== Function ==
	The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :		The protein have a role of transferase, more accurately it is a NDP-glucose--starch glucosyltransferase, which catalyse the reaction below :
-	[[Image:~~reaction~~.jpg]]	+	[[Image:Catalytic activity 3vuf'.jpg]]
		+
	This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.		This is a reaction allowing the extension of amylose. It has a major role in the pathway starch biosynthesis.