6ils - Revision history

OCA at 09:45, 22 November 2023

OCA — Wed, 22 Nov 2023 09:45:48 GMT

←Older revision		Revision as of 09:45, 22 November 2023
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	<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ils]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ILS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ils]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ILS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ATP:ADENOSINE~~-~~5-TRIPHOSPHATE'>ATP</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~At1g17160, F20D23.14, F20D23_14 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=3702 ARATH])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15]~~ </~~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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [https://pdbe.org/6ils PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [https://www.ebi.ac.uk/pdbsum/6ils PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils 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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [~~http~~://pdbe.org/6ils PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ils PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A1A6H3_ARATH A1A6H3_ARATH]~~] Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.[HAMAP-Rule:MF_03215]	+	[https://www.uniprot.org/uniprot/RBSK_ARATH RBSK_ARATH] Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway (By similarity) (PubMed:27601466). Can also use xylose and fructose as carbohydrate substrates with a low efficiency (PubMed:27601466). Can use GTP, and, to a lower extent, CTP and UTP as alternative phosphoryl donors (PubMed:27601466).[HAMAP-Rule:MF_03215]<ref>PMID:27601466</ref>
	<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 6ils" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ils" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribokinase\|Ribokinase]]
		+	*[[Ribokinase 3D structures\|Ribokinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribokinase]]~~	+	[[Category: Kang P]]
-	[[Category: Kang, P]]	+	[[Category: Oh J]]
-	[[Category: Oh, J]]	+	[[Category: Rhee S]]
-	[[Category: Rhee, S]]	+
-	~~[[Category: Atrbsk]]~~	+
-	~~[[Category: Pfkb family]]~~	+
-	~~[[Category: Phosphotransferase]]~~	+
-	~~[[Category: Ribose]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:14, 24 April 2019

OCA — Wed, 24 Apr 2019 08:14:33 GMT

←Older revision		Revision as of 08:14, 24 April 2019
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	<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ils]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ils]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At1g17160, F20D23.14, F20D23_14 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15] </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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [http://pdbe.org/6ils PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [http://www.ebi.ac.uk/pdbsum/6ils PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils 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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [http://pdbe.org/6ils PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [http://www.ebi.ac.uk/pdbsum/6ils PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ribokinase]]		[[Category: Ribokinase]]

OCA at 12:05, 13 March 2019

OCA — Wed, 13 Mar 2019 12:05:17 GMT

←Older revision		Revision as of 12:05, 13 March 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6ils is ~~ON HOLD until Paper~~ Publication	+	==Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP==
		+	<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ils]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15] </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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [http://pdbe.org/6ils PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [http://www.ebi.ac.uk/pdbsum/6ils PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A1A6H3_ARATH A1A6H3_ARATH]] Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.[HAMAP-Rule:MF_03215]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides. In this study, we report the crystal structure of RBSK from Arapidopsis thaliana (AtRBSK) in three different ligation states: an unliganded state, a ternary complex with ribose and ATP, and a binary complex with ATP in the presence of Mg(2+). In the monomeric conformation, AtRBSK is highly homologous to bacterial RBSKs, including the binding sites for a monovalent cation, ribose, and ATP. Its dimeric conformation, however, does not exhibit the noticeable ligand-induced changes that were observed in bacterial orthologs. Only in the presence of Mg(2+), ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg(2+) in AtRBSK activity. The structural data combined with activity analyses of mutants allowed assignment of functional roles for the active site residues. Overall, this study provides the first structural characterization of plant RBSK, and experimentally validates a previous hypothetical model concerning the general reaction mechanism of RBSK.

-	~~Authors: Kang, P~~., Oh, J., ~~Rhee~~, S.	+	Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.,Kang PA, Oh J, Lee H, Witte CP, Rhee S J Struct Biol. 2019 Feb 26. pii: S1047-8477(19)30030-9. doi:, 10.1016/j.jsb.2019.02.007. PMID:30822455<ref>PMID:30822455</ref>

-	~~Description: Structure~~ of ~~Arabidopsis thaliana Ribokinase complexed with Ribose and ATP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ils" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ribokinase]]
	[[Category: Kang, P]]		[[Category: Kang, P]]
-	[[Category: Rhee, S]]
	[[Category: Oh, J]]		[[Category: Oh, J]]
		+	[[Category: Rhee, S]]
		+	[[Category: Atrbsk]]
		+	[[Category: Pfkb family]]
		+	[[Category: Phosphotransferase]]
		+	[[Category: Ribose]]
		+	[[Category: Transferase]]

OCA at 18:50, 2 December 2018

OCA — Sun, 02 Dec 2018 18:50:30 GMT

←Older revision		Revision as of 18:50, 2 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kang, P., Oh, J., Rhee, S.		Authors: Kang, P., Oh, J., Rhee, S.
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	Description: Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP		Description: Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kang, P]]
	[[Category: Rhee, S]]		[[Category: Rhee, S]]
	[[Category: Oh, J]]		[[Category: Oh, J]]
-	[[Category: Kang, P]]

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

OCA — Wed, 24 Oct 2018 04:26:24 GMT

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

←Older revision

Revision as of 04:26, 24 October 2018

OCA: New page: '''Unreleased structure''' The entry 6ils is ON HOLD Authors: Kang, P., Oh, J., Rhee, S. Description: Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP [[Categ...

OCA — Wed, 24 Oct 2018 04:26:21 GMT

New page: '''Unreleased structure''' The entry 6ils is ON HOLD Authors: Kang, P., Oh, J., Rhee, S. Description: Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP [[Categ...

New page

'''Unreleased structure'''

The entry 6ils is ON HOLD

Authors: Kang, P., Oh, J., Rhee, S.

Description: Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP
[[Category: Unreleased Structures]]
[[Category: Rhee, S]]
[[Category: Oh, J]]
[[Category: Kang, P]]