5ya2 - Revision history

OCA at 10:22, 27 March 2024

OCA — Wed, 27 Mar 2024 10:22:27 GMT

←Older revision		Revision as of 10:22, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5ya2' size='340' side='right'caption='[[5ya2]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5ya2' size='340' side='right'caption='[[5ya2]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ya2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YA2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ya2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YA2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.701Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Autoinducer-2_kinase Autoinducer-2 kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.189 2.7.1.189] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ya2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya2 OCA], [~~http~~://pdbe.org/5ya2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ya2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ya2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya2 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=5ya2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya2 OCA], [https://pdbe.org/5ya2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ya2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ya2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LSRK_ECOLI LSRK_ECOLI]] Catalyzes the phosphorylation of autoinducer-2 (AI-2) to phospho-AI-2, which subsequently inactivates the transcriptional regulator LsrR and leads to the transcription of the lsr operon. Phosphorylates the ring-open form of (S)-4,5-dihydroxypentane-2,3-dione (DPD), which is the precursor to all AI-2 signaling molecules, at the C5 position. Required for the regulation of the lsr operon and many other genes.<ref>PMID:15601708</ref> <ref>PMID:17557827</ref> <ref>PMID:20025244</ref> [[http://www.uniprot.org/uniprot/PTHP_ECOLI PTHP_ECOLI]] General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate (PEP) is transferred to the phosphoryl carrier protein HPr by enzyme I. Phospho-HPr then transfers it to the permease (enzymes II/III).	+	[https://www.uniprot.org/uniprot/LSRK_ECOLI LSRK_ECOLI] Catalyzes the phosphorylation of autoinducer-2 (AI-2) to phospho-AI-2, which subsequently inactivates the transcriptional regulator LsrR and leads to the transcription of the lsr operon. Phosphorylates the ring-open form of (S)-4,5-dihydroxypentane-2,3-dione (DPD), which is the precursor to all AI-2 signaling molecules, at the C5 position. Required for the regulation of the lsr operon and many other genes.<ref>PMID:15601708</ref> <ref>PMID:17557827</ref> <ref>PMID:20025244</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Quorum sensing (QS), a bacterial process that regulates population-scale behavior, is mediated by small signaling molecules, called autoinducers (AIs), that are secreted and perceived, modulating a "collective" phenotype. Because the autoinducer AI-2 is secreted by a wide variety of bacterial species, its "perception" cues bacterial behavior. This response is mediated by the lsr (LuxS-regulated) operon that includes the AI-2 transporter LsrACDB and the kinase LsrK. We report that HPr, a phosphocarrier protein central to the sugar phosphotransferase system of Escherichia coli, copurifies with LsrK. Cocrystal structures of an LsrK/HPr complex were determined, and the effects of HPr and phosphorylated HPr on LsrK activity were assessed. LsrK activity is inhibited when bound to HPr, revealing new linkages between QS activity and sugar metabolism. These findings help shed new light on the abilities of bacteria to rapidly respond to changing nutrient levels at the population scale. They also suggest new means of manipulating QS activity among bacteria and within various niches.	+
-		+
-	Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr.,Ha JH, Hauk P, Cho K, Eo Y, Ma X, Stephens K, Cha S, Jeong M, Suh JY, Sintim HO, Bentley WE, Ryu KS Sci Adv. 2018 Jun 1;4(6):eaar7063. doi: 10.1126/sciadv.aar7063. eCollection 2018 , Jun. PMID:29868643<ref>PMID:29868643</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ya2" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 26:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Autoinducer~~-~~2 kinase~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ha~~, J H~~]]	+	[[Category: Ha JH]]
-	[[Category: Ryu~~, K S]]~~	+	[[Category: Ryu KS]]
-	~~[[Category: Adp binding]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Hpr]]~~	+
-	~~[[Category: Lsrk]]~~	+
-	~~[[Category: Quorum sensing]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 09:14, 21 October 2020

OCA — Wed, 21 Oct 2020 09:14:26 GMT

←Older revision		Revision as of 09:14, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of LsrK-HPr complex with ADP==		==Crystal structure of LsrK-HPr complex with ADP==
-	<StructureSection load='5ya2' size='340' side='right' caption='[[5ya2]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5ya2' size='340' side='right'caption='[[5ya2]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ya2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YA2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ya2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YA2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Autoinducer-2_kinase Autoinducer-2 kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.189 2.7.1.189] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Autoinducer-2_kinase Autoinducer-2 kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.189 2.7.1.189] </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=5ya2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya2 OCA], [http://pdbe.org/5ya2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ya2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya2 OCA], [http://pdbe.org/5ya2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ya2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ya2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphocarrier protein HPr 3D structures\|Phosphocarrier protein HPr 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Autoinducer-2 kinase]]		[[Category: Autoinducer-2 kinase]]
		+	[[Category: Large Structures]]
	[[Category: Ha, J H]]		[[Category: Ha, J H]]
	[[Category: Ryu, K S]]		[[Category: Ryu, K S]]

OCA at 05:39, 11 July 2018

OCA — Wed, 11 Jul 2018 05:39:26 GMT

←Older revision		Revision as of 05:39, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ya2 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of LsrK-HPr complex with ADP==
		+	<StructureSection load='5ya2' size='340' side='right' caption='[[5ya2]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ya2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YA2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YA2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Autoinducer-2_kinase Autoinducer-2 kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.189 2.7.1.189] </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=5ya2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ya2 OCA], [http://pdbe.org/5ya2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ya2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ya2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ya2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LSRK_ECOLI LSRK_ECOLI]] Catalyzes the phosphorylation of autoinducer-2 (AI-2) to phospho-AI-2, which subsequently inactivates the transcriptional regulator LsrR and leads to the transcription of the lsr operon. Phosphorylates the ring-open form of (S)-4,5-dihydroxypentane-2,3-dione (DPD), which is the precursor to all AI-2 signaling molecules, at the C5 position. Required for the regulation of the lsr operon and many other genes.<ref>PMID:15601708</ref> <ref>PMID:17557827</ref> <ref>PMID:20025244</ref> [[http://www.uniprot.org/uniprot/PTHP_ECOLI PTHP_ECOLI]] General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate (PEP) is transferred to the phosphoryl carrier protein HPr by enzyme I. Phospho-HPr then transfers it to the permease (enzymes II/III).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Quorum sensing (QS), a bacterial process that regulates population-scale behavior, is mediated by small signaling molecules, called autoinducers (AIs), that are secreted and perceived, modulating a "collective" phenotype. Because the autoinducer AI-2 is secreted by a wide variety of bacterial species, its "perception" cues bacterial behavior. This response is mediated by the lsr (LuxS-regulated) operon that includes the AI-2 transporter LsrACDB and the kinase LsrK. We report that HPr, a phosphocarrier protein central to the sugar phosphotransferase system of Escherichia coli, copurifies with LsrK. Cocrystal structures of an LsrK/HPr complex were determined, and the effects of HPr and phosphorylated HPr on LsrK activity were assessed. LsrK activity is inhibited when bound to HPr, revealing new linkages between QS activity and sugar metabolism. These findings help shed new light on the abilities of bacteria to rapidly respond to changing nutrient levels at the population scale. They also suggest new means of manipulating QS activity among bacteria and within various niches.

-	~~Authors: Ryu~~, K.S., Ha, J.H.	+	Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr.,Ha JH, Hauk P, Cho K, Eo Y, Ma X, Stephens K, Cha S, Jeong M, Suh JY, Sintim HO, Bentley WE, Ryu KS Sci Adv. 2018 Jun 1;4(6):eaar7063. doi: 10.1126/sciadv.aar7063. eCollection 2018 , Jun. PMID:29868643<ref>PMID:29868643</ref>

-	~~Description: Crystal structure~~ of ~~LsrK~~-~~HPr complex with ADP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Ha, J.H]]	+	<div class="pdbe-citations 5ya2" style="background-color:#fffaf0;"></div>
-	[[Category: Ryu, K.S]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Autoinducer-2 kinase]]
		+	[[Category: Ha, J H]]
		+	[[Category: Ryu, K S]]
		+	[[Category: Adp binding]]
		+	[[Category: Complex]]
		+	[[Category: Hpr]]
		+	[[Category: Lsrk]]
		+	[[Category: Quorum sensing]]
		+	[[Category: Structural protein]]

OCA: Protected "5ya2" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:19:32 GMT

Protected "5ya2" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:19, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ya2 is ON HOLD until Paper Publication Authors: Ryu, K.S., Ha, J.H. Description: Crystal structure of LsrK-HPr complex with ADP [[Category: Unrele...

OCA — Wed, 27 Sep 2017 16:19:31 GMT

New page: '''Unreleased structure''' The entry 5ya2 is ON HOLD until Paper Publication Authors: Ryu, K.S., Ha, J.H. Description: Crystal structure of LsrK-HPr complex with ADP [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5ya2 is ON HOLD until Paper Publication

Authors: Ryu, K.S., Ha, J.H.

Description: Crystal structure of LsrK-HPr complex with ADP
[[Category: Unreleased Structures]]
[[Category: Ha, J.H]]
[[Category: Ryu, K.S]]