3t9d - Revision history

OCA at 10:06, 1 March 2024

OCA — Fri, 01 Mar 2024 10:06:39 GMT

←Older revision		Revision as of 10:06, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3t9d' size='340' side='right'caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3t9d' size='340' side='right'caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.85Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [https://pdbe.org/3t9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [https://www.ebi.ac.uk/pdbsum/3t9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t9d 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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [https://pdbe.org/3t9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [https://www.ebi.ac.uk/pdbsum/3t9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>	+	[https://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domain of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF(3)(-) transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.	+
-		+
-	Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.,Wang H, Falck JR, Hall TM, Shears SB Nat Chem Biol. 2011 Nov 27. doi: 10.1038/nchembio.733. PMID:22119861<ref>PMID:22119861</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3t9d" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Diphosphoinositol-pentakisphosphate kinase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Falck, J]]	+	[[Category: Falck J]]
-	[[Category: Hall~~, T M.T~~]]	+	[[Category: Hall TMT]]
-	[[Category: Shears~~, S B~~]]	+	[[Category: Shears SB]]
-	[[Category: Wang, H]]	+	[[Category: Wang H]]
-	~~[[Category: Atp-grasp fold]]~~	+
-	~~[[Category: Inositol pyrophosphate kinase]]~~	+
-	~~[[Category: Phosphoryl transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 16:48, 6 July 2022

OCA — Wed, 06 Jul 2022 16:48:32 GMT

←Older revision		Revision as of 16:48, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)==		==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)==
-	<StructureSection load='3t9d' size='340' side='right' caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3t9d' size='340' side='right'caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [~~http~~://pdbe.org/3t9d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t9d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t9d 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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [https://pdbe.org/3t9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [https://www.ebi.ac.uk/pdbsum/3t9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>	+	[[https://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	[[Category: Diphosphoinositol-pentakisphosphate kinase]]		[[Category: Diphosphoinositol-pentakisphosphate kinase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Falck, J]]		[[Category: Falck, J]]
	[[Category: Hall, T M.T]]		[[Category: Hall, T M.T]]

OCA at 08:39, 5 August 2016

OCA — Fri, 05 Aug 2016 08:39:23 GMT

←Older revision		Revision as of 08:39, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)==		==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)==
	<StructureSection load='3t9d' size='340' side='right' caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3t9d' size='340' side='right' caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T9D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [http://www.ebi.ac.uk/pdbsum/3t9d 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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [http://pdbe.org/3t9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [http://www.ebi.ac.uk/pdbsum/3t9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3t9d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Diphosphoinositol-pentakisphosphate kinase]]		[[Category: Diphosphoinositol-pentakisphosphate kinase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Falck, J]]		[[Category: Falck, J]]
	[[Category: Hall, T M.T]]		[[Category: Hall, T M.T]]

OCA at 00:50, 25 December 2014

OCA — Thu, 25 Dec 2014 00:50:55 GMT

←Older revision		Revision as of 00:50, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T9D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [http://www.ebi.ac.uk/pdbsum/3t9d 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=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [http://www.ebi.ac.uk/pdbsum/3t9d PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VIP2_HUMAN VIP2_HUMAN]] Bifunctional inositol kinase that acts in concert with the IP6K kinases IP6K1, IP6K2 and IP6K3 to synthesize the diphosphate group-containing inositol pyrophosphates diphosphoinositol pentakisphosphate, PP-InsP5, and bis-diphosphoinositol tetrakisphosphate, (PP)2-InsP4. PP-InsP5 and (PP)2-InsP4, also respectively called InsP7 and InsP8, regulate a variety of cellular processes, including apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, insulin signaling and neutrophil activation. Phosphorylates inositol hexakisphosphate (InsP6) at positions 1 or 3 to produce PP-InsP5 which is in turn phosphorylated by IP6Ks to produce (PP)2-InsP4. Alternatively, phosphorylates at position 1 or 3 PP-InsP5, produced by IP6Ks from InsP6, to produce (PP)2-InsP4.<ref>PMID:17690096</ref> <ref>PMID:17702752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.,Wang H, Falck JR, Hall TM, Shears SB Nat Chem Biol. 2011 Nov 27. doi: 10.1038/nchembio.733. PMID:22119861<ref>PMID:22119861</ref>		Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.,Wang H, Falck JR, Hall TM, Shears SB Nat Chem Biol. 2011 Nov 27. doi: 10.1038/nchembio.733. PMID:22119861<ref>PMID:22119861</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Diphosphoinositol-pentakisphosphate kinase]]		[[Category: Diphosphoinositol-pentakisphosphate kinase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Falck, J.]]	+	[[Category: Falck, J]]
-	[[Category: Hall, T M.T.]]	+	[[Category: Hall, T M.T]]
-	[[Category: Shears, S B.]]	+	[[Category: Shears, S B]]
-	[[Category: Wang, H.]]	+	[[Category: Wang, H]]
	[[Category: Atp-grasp fold]]		[[Category: Atp-grasp fold]]
	[[Category: Inositol pyrophosphate kinase]]		[[Category: Inositol pyrophosphate kinase]]
	[[Category: Phosphoryl transferase]]		[[Category: Phosphoryl transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:22, 5 June 2014

OCA — Thu, 05 Jun 2014 06:22:06 GMT

←Older revision		Revision as of 06:22, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3t9d.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)==
		+	<StructureSection load='3t9d' size='340' side='right' caption='[[3t9d]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T9D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=I7P:(1R,2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY)CYCLOHEXYL+TRIHYDROGEN+DIPHOSPHATE'>I7P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t54\|3t54]], [[3t7a\|3t7a]], [[3t99\|3t99]], [[3t9a\|3t9a]], [[3t9b\|3t9b]], [[3t9c\|3t9c]], [[3t9e\|3t9e]], [[3t9f\|3t9f]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIP5K2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diphosphoinositol-pentakisphosphate_kinase Diphosphoinositol-pentakisphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.24 2.7.4.24] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t9d RCSB], [http://www.ebi.ac.uk/pdbsum/3t9d PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inositol pyrophosphates (such as IP7 and IP8) are multifunctional signaling molecules that regulate diverse cellular activities. Inositol pyrophosphates have 'high-energy' phosphoanhydride bonds, so their enzymatic synthesis requires that a substantial energy barrier to the transition state be overcome. Additionally, inositol pyrophosphate kinases can show stringent ligand specificity, despite the need to accommodate the steric bulk and intense electronegativity of nature's most concentrated three-dimensional array of phosphate groups. Here we examine how these catalytic challenges are met by describing the structure and reaction cycle of an inositol pyrophosphate kinase at the atomic level. We obtained crystal structures of the kinase domain of human PPIP5K2 complexed with nucleotide cofactors and either substrates, product or a MgF(3)(-) transition-state mimic. We describe the enzyme's conformational dynamics, its unprecedented topological presentation of nucleotide and inositol phosphate, and the charge balance that facilitates partly associative in-line phosphoryl transfer.

-	~~<!--~~	+	Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding.,Wang H, Falck JR, Hall TM, Shears SB Nat Chem Biol. 2011 Nov 27. doi: 10.1038/nchembio.733. PMID:22119861<ref>PMID:22119861</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3t9d"~~, ~~creates the "Structure Box" on the page.~~	+
-	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded)~~,	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3t9d\| PDB=3t9d \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22119861}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22119861 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22119861}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3t9d]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022119861<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Diphosphoinositol-pentakisphosphate kinase]]		[[Category: Diphosphoinositol-pentakisphosphate kinase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 10:41, 14 December 2011

OCA — Wed, 14 Dec 2011 10:41:14 GMT

←Older revision		Revision as of 10:41, 14 December 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3t9d.png\|left\|200px]]

-	The ~~entry 3t9d~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t9d", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3t9d\| PDB=3t9d \| SCENE= }}

-	~~Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B.~~	+	===Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)===

-	~~Description: Crystal structure of~~ the ~~catalytic domain of human diphosphoinositol pentakisphosphate kinase 2~~ (~~PPIP5K2~~) ~~in complex~~ with ~~AMPPNP and 5~~-~~(PP)~~-~~IP5 (5~~-~~IP7)~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22119861}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22119861 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22119861}}
		+
		+	==About this Structure==
		+	[[3t9d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T9D OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022119861</ref><references group="xtra"/>
		+	[[Category: Diphosphoinositol-pentakisphosphate kinase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Falck, J.]]
		+	[[Category: Hall, T M.T.]]
		+	[[Category: Shears, S B.]]
		+	[[Category: Wang, H.]]
		+	[[Category: Atp-grasp fold]]
		+	[[Category: Inositol pyrophosphate kinase]]
		+	[[Category: Phosphoryl transferase]]
		+	[[Category: Transferase]]

OCA at 05:55, 17 August 2011

OCA — Wed, 17 Aug 2011 05:55:14 GMT

←Older revision		Revision as of 05:55, 17 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3t9d is ON HOLD	+	The entry 3t9d is ON HOLD until Paper Publication

	Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B.		Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B.

	Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)		Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)

OCA: Protected "3t9d" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2011 05:38:03 GMT

Protected "3t9d" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 10 August 2011

OCA: New page: '''Unreleased structure''' The entry 3t9d is ON HOLD Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B. Description: Crystal structure of the catalytic domain of human diphosphoi...

OCA — Wed, 10 Aug 2011 05:38:02 GMT

New page: '''Unreleased structure''' The entry 3t9d is ON HOLD Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B. Description: Crystal structure of the catalytic domain of human diphosphoi...

New page

'''Unreleased structure'''

The entry 3t9d is ON HOLD

Authors: Wang, H., Falck, J., Hall, T.M.T., Shears, S.B.

Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)