5llb - Revision history

OCA at 18:33, 18 October 2023

OCA — Wed, 18 Oct 2023 18:33:03 GMT

←Older revision		Revision as of 18:33, 18 October 2023
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	<StructureSection load='5llb' size='340' side='right'caption='[[5llb]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='5llb' size='340' side='right'caption='[[5llb]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Fratt Fratt~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LLB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Francisella_tularensis_subsp._tularensis_SCHU_S4 Francisella tularensis subsp. tularensis SCHU S4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LLB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6YW:[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]+phosphono+hydrogen+phosphate'>6YW</scene>, <scene name='pdbligand=6YZ:[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic+acid'>6YZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.92Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yeg\|4yeg]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6YW:[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]+phosphono+hydrogen+phosphate'>6YW</scene>, <scene name='pdbligand=6YZ:[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic+acid'>6YZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">ppk2, FTT_1564, BZ14_1190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=177416 FRATT])</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=5llb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llb OCA], [https://pdbe.org/5llb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5llb RCSB], [https://www.ebi.ac.uk/pdbsum/5llb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5llb ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polyphosphate_kinase Polyphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.1 2.7.4.1] </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=5llb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llb OCA], [~~http~~://pdbe.org/5llb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5llb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5llb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5llb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5NEQ5_FRATT Q5NEQ5_FRATT]
	<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: ~~Fratt~~]]	+	[[Category: Francisella tularensis subsp. tularensis SCHU S4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Polyphosphate kinase]]~~	+	[[Category: Parnell AE]]
-	[[Category: Parnell~~, A E~~]]	+	[[Category: Roach PL]]
-	[[Category: Roach~~, P L]]~~	+
-	~~[[Category: Complex with non-hydrolysable atp analogue. polyphosphate metabolism. nucleotide metabolism]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:29, 16 October 2019

OCA — Wed, 16 Oct 2019 06:29:59 GMT

←Older revision		Revision as of 06:29, 16 October 2019
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	==Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate==		==Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate==
-	<StructureSection load='5llb' size='340' side='right' caption='[[5llb]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='5llb' size='340' side='right'caption='[[5llb]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fratt Fratt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fratt Fratt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLB FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Fratt]]		[[Category: Fratt]]
		+	[[Category: Large Structures]]
	[[Category: Polyphosphate kinase]]		[[Category: Polyphosphate kinase]]
	[[Category: Parnell, A E]]		[[Category: Parnell, A E]]

OCA at 08:25, 3 October 2018

OCA — Wed, 03 Oct 2018 08:25:06 GMT

←Older revision		Revision as of 08:25, 3 October 2018
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fratt Fratt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fratt Fratt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6YW:[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]+phosphono+hydrogen+phosphate'>6YW</scene>, <scene name='pdbligand=6YZ:[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-~~bis(~~oxidanyl)-~~$l^{5}-phosphanyl]methyl-bis~~(~~oxidanyl~~)-~~$l^{5}-phosphanyl~~]+~~phosphono+hydrogen+phosphate~~'>6YZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6YW:[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]+phosphono+hydrogen+phosphate'>6YW</scene>, <scene name='pdbligand=6YZ:[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]methyl]phosphinic+acid'>6YZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">[[4yeg\|4yeg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yeg\|4yeg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppk2, FTT_1564, BZ14_1190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=177416 FRATT])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppk2, FTT_1564, BZ14_1190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=177416 FRATT])</td></tr>

OCA at 07:53, 21 March 2018

OCA — Wed, 21 Mar 2018 07:53:20 GMT

←Older revision		Revision as of 07:53, 21 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5llb is ~~ON HOLD until Paper~~ Publication	+	==Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate==
		+	<StructureSection load='5llb' size='340' side='right' caption='[[5llb]], [[Resolution\|resolution]] 1.92Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5llb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fratt Fratt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6YW:[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl]+phosphono+hydrogen+phosphate'>6YW</scene>, <scene name='pdbligand=6YZ:[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-bis(oxidanyl)-$l^{5}-phosphanyl]methyl-bis(oxidanyl)-$l^{5}-phosphanyl]+phosphono+hydrogen+phosphate'>6YZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">[[4yeg\|4yeg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ppk2, FTT_1564, BZ14_1190 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=177416 FRATT])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polyphosphate_kinase Polyphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.1 2.7.4.1] </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=5llb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llb OCA], [http://pdbe.org/5llb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5llb RCSB], [http://www.ebi.ac.uk/pdbsum/5llb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5llb ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energy-rich phosphoanhydride bonds. Polyphosphate kinases of the family 2 (PPK2) use polyphosphate to catalyze the reversible phosphorylation of nucleotide phosphates and are highly relevant as targets for new pharmaceutical compounds and as biocatalysts for cofactor regeneration. PPK2s can be classified based on their preference for nucleoside mono- or diphosphates or both. The detailed mechanism of PPK2s and the molecular basis for their substrate preference is unclear, which is mainly due to the lack of high-resolution structures with substrates or substrate analogs. Here, we report the structural analysis and comparison of a class I PPK2 (ADP-phosphorylating) and a class III PPK2 (AMP- and ADP-phosphorylating), both complexed with polyphosphate and/or nucleotide substrates. Together with complementary biochemical analyses, these define the molecular basis of nucleotide specificity and are consistent with a Mg(2+) catalyzed in-line phosphoryl transfer mechanism. This mechanistic insight will guide the development of PPK2 inhibitors as potential antibacterials or genetically modified PPK2s that phosphorylate alternative substrates.

-	~~Authors~~:	+	Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.,Parnell AE, Mordhorst S, Kemper F, Giurrandino M, Prince JP, Schwarzer NJ, Hofer A, Wohlwend D, Jessen HJ, Gerhardt S, Einsle O, Oyston PCF, Andexer JN, Roach PL Proc Natl Acad Sci U S A. 2018 Mar 12. pii: 1710741115. doi:, 10.1073/pnas.1710741115. PMID:29531036<ref>PMID:29531036</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5llb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fratt]]
		+	[[Category: Polyphosphate kinase]]
		+	[[Category: Parnell, A E]]
		+	[[Category: Roach, P L]]
		+	[[Category: Complex with non-hydrolysable atp analogue. polyphosphate metabolism. nucleotide metabolism]]
		+	[[Category: Transferase]]

OCA: Protected "5llb" [edit=sysop:move=sysop]

OCA — Thu, 04 Aug 2016 02:57:10 GMT

Protected "5llb" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:57, 4 August 2016

OCA: New page: '''Unreleased structure''' The entry 5llb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 04 Aug 2016 02:57:09 GMT

New page: '''Unreleased structure''' The entry 5llb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5llb is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]