OCA at 11:01, 3 January 2024

2024-01-03T11:01:44Z

←Older revision		Revision as of 11:01, 3 January 2024
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-	'''Unreleased structure'''

-	~~The entry~~ 8g9e is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7==
		+	<StructureSection load='8g9e' size='340' side='right'caption='[[8g9e]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8g9e]] 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=8G9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8G9E FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.75Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YUT:{difluoro[(R)-hydroxy{[(1s,2R,3S,4S,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic+acid'>YUT</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=8g9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8g9e OCA], [https://pdbe.org/8g9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8g9e RCSB], [https://www.ebi.ac.uk/pdbsum/8g9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8g9e ProSAT]</span></td></tr>
		+	</table>
		+	== 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP(5) is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP(5) . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.

-	~~Authors: Wang~~, H., Shears, S.B.	+	Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs.,Hostachy S, Wang H, Zong G, Franke K, Riley AM, Schmieder P, Potter BVL, Shears SB, Fiedler D Chemistry. 2023 Dec 1;29(67):e202302426. doi: 10.1002/chem.202302426. Epub 2023 , Oct 19. PMID:37773020<ref>PMID:37773020</ref>

-	~~Description: Crystal structure~~ of the ~~catalytic domain~~ of ~~human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP~~-~~PNP and 5~~-~~(PCF2P)-IP5, an analog of 5-IP7~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Shears~~, S.B~~]]	+	<div class="pdbe-citations 8g9e" style="background-color:#fffaf0;"></div>
-	[[Category: Wang, H]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Shears SB]]
		+	[[Category: Wang H]]

OCA at 04:12, 6 September 2023

2023-09-06T04:12:29Z

←Older revision		Revision as of 04:12, 6 September 2023
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	Authors: Wang, H., Shears, S.B.		Authors: Wang, H., Shears, S.B.

-	Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(~~PCP~~)-IP5	+	Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCF2P)-IP5, an analog of 5-IP7
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Shears, S.B]]		[[Category: Shears, S.B]]
	[[Category: Wang, H]]		[[Category: Wang, H]]

OCA at 05:45, 8 March 2023

2023-03-08T05:45:23Z

←Older revision		Revision as of 05:45, 8 March 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8g9e is ON HOLD	+	The entry 8g9e is ON HOLD until Paper Publication

	Authors: Wang, H., Shears, S.B.		Authors: Wang, H., Shears, S.B.

OCA: Protected "8g9e" [edit=sysop:move=sysop]

2023-03-02T04:32:03Z

Protected "8g9e" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:32, 2 March 2023

OCA: New page: '''Unreleased structure''' The entry 8g9e is ON HOLD Authors: Wang, H., Shears, S.B. Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate...

2023-03-02T04:32:02Z

New page: '''Unreleased structure''' The entry 8g9e is ON HOLD Authors: Wang, H., Shears, S.B. Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate...

New page

'''Unreleased structure'''

The entry 8g9e is ON HOLD

Authors: Wang, H., Shears, S.B.

Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5
[[Category: Unreleased Structures]]
[[Category: Shears, S.B]]
[[Category: Wang, H]]

8g9e - Revision history

OCA at 11:01, 3 January 2024

OCA at 04:12, 6 September 2023

OCA at 05:45, 8 March 2023

OCA: Protected "8g9e" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8g9e is ON HOLD Authors: Wang, H., Shears, S.B. Description: Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate...