7em2 - Revision history

OCA at 16:56, 29 November 2023

OCA — Wed, 29 Nov 2023 16:56:19 GMT

←Older revision		Revision as of 16:56, 29 November 2023
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	<StructureSection load='7em2' size='340' side='right'caption='[[7em2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='7em2' size='340' side='right'caption='[[7em2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7em2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7em2]] is a 2 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=7EM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EM2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CZC:[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+phosphono+hydrogen+phosphate'>CZC</scene>, <scene name='pdbligand=CZF:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>CZF</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]] 2.6Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1-phosphatidylinositol-5-phosphate_4-kinase 1-phosphatidylinositol-5-phosphate 4-kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.149 2.7.1.149] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CZC:[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+phosphono+hydrogen+phosphate'>CZC</scene>, <scene name='pdbligand=CZF:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>CZF</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=7em2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7em2 OCA], [https://pdbe.org/7em2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7em2 RCSB], [https://www.ebi.ac.uk/pdbsum/7em2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7em2 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=7em2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7em2 OCA], [https://pdbe.org/7em2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7em2 RCSB], [https://www.ebi.ac.uk/pdbsum/7em2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7em2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PI42B_HUMAN PI42B_HUMAN]] Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate.<ref>PMID:9038203</ref>	+	[https://www.uniprot.org/uniprot/PI42B_HUMAN PI42B_HUMAN] Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate.<ref>PMID:9038203</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~1-phosphatidylinositol-5-phosphate 4-kinase~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Senda, M]]	+	[[Category: Senda M]]
-	[[Category: Senda, T]]	+	[[Category: Senda T]]
-	~~[[Category: Lipid kinase]]~~	+
-	~~[[Category: Phosphoinositide signaling]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:11, 25 May 2022

OCA — Wed, 25 May 2022 08:11:11 GMT

←Older revision		Revision as of 08:11, 25 May 2022
Line 10:		Line 10:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PI42B_HUMAN PI42B_HUMAN]] Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate.<ref>PMID:9038203</ref>		[[https://www.uniprot.org/uniprot/PI42B_HUMAN PI42B_HUMAN]] Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate.<ref>PMID:9038203</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase beta (PI5P4Kbeta) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kbeta has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128 G proteins has uncovered that most kinases and PI5P4Kbeta use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kbeta has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.
		+
		+	The GTP responsiveness of PI5P4Kbeta evolved from a compromised trade-off between activity and specificity.,Takeuchi K, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT, Senda T Structure. 2022 Apr 18. pii: S0969-2126(22)00131-9. doi:, 10.1016/j.str.2022.04.004. PMID:35504278<ref>PMID:35504278</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7em2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:30, 6 April 2022

OCA — Wed, 06 Apr 2022 10:30:40 GMT

←Older revision		Revision as of 10:30, 6 April 2022
Line 1:		Line 1:

	==Crystal structure of the PI5P4Kbeta-XTP complex==		==Crystal structure of the PI5P4Kbeta-XTP complex==
-	<StructureSection load='7em2' size='340' side='right'caption='[[7em2]]' scene=''>	+	<StructureSection load='7em2' size='340' side='right'caption='[[7em2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EM2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7em2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EM2 FirstGlance]. <br>
-	</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=7em2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7em2 OCA], [https://pdbe.org/7em2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7em2 RCSB], [https://www.ebi.ac.uk/pdbsum/7em2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7em2 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CZC:[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+phosphono+hydrogen+phosphate'>CZC</scene>, <scene name='pdbligand=CZF:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>CZF</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1-phosphatidylinositol-5-phosphate_4-kinase 1-phosphatidylinositol-5-phosphate 4-kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.149 2.7.1.149] </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=7em2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7em2 OCA], [https://pdbe.org/7em2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7em2 RCSB], [https://www.ebi.ac.uk/pdbsum/7em2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7em2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PI42B_HUMAN PI42B_HUMAN]] Participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate.<ref>PMID:9038203</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 1-phosphatidylinositol-5-phosphate 4-kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Senda M]]	+	[[Category: Senda, M]]
-	[[Category: Senda T]]	+	[[Category: Senda, T]]
		+	[[Category: Lipid kinase]]
		+	[[Category: Phosphoinositide signaling]]
		+	[[Category: Transferase]]

OCA at 10:44, 30 March 2022

OCA — Wed, 30 Mar 2022 10:44:32 GMT

←Older revision		Revision as of 10:44, 30 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7em2 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the PI5P4Kbeta-XTP complex==
-		+	<StructureSection load='7em2' size='340' side='right'caption='[[7em2]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EM2 FirstGlance]. <br>
-	~~Description~~:	+	</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=7em2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7em2 OCA], [https://pdbe.org/7em2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7em2 RCSB], [https://www.ebi.ac.uk/pdbsum/7em2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7em2 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Senda M]]
		+	[[Category: Senda T]]

OCA at 07:17, 5 May 2021

OCA — Wed, 05 May 2021 07:17:15 GMT

←Older revision		Revision as of 07:17, 5 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7em2 is ON HOLD	+	The entry 7em2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7em2" [edit=sysop:move=sysop]

OCA — Wed, 21 Apr 2021 06:05:42 GMT

Protected "7em2" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:05, 21 April 2021

OCA: New page: '''Unreleased structure''' The entry 7em2 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Apr 2021 06:05:41 GMT

New page: '''Unreleased structure''' The entry 7em2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7em2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]