5z5r - Revision history

OCA at 10:35, 14 June 2023

OCA — Wed, 14 Jun 2023 10:35:04 GMT

←Older revision		Revision as of 10:35, 14 June 2023
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	==Nukacin ISK-1 in inactive state==		==Nukacin ISK-1 in inactive state==
-	<StructureSection load='5z5r' size='340' side='right'caption='[[5z5r~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5z5r' size='340' side='right'caption='[[5z5r]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z5R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z5R FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</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=5z5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5r OCA], [~~http~~://pdbe.org/5z5r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z5r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z5r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5r 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=5z5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5r OCA], [https://pdbe.org/5z5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z5r RCSB], [https://www.ebi.ac.uk/pdbsum/5z5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LANNA_STAWA LANNA_STAWA]] Lanthionine-containing peptide antibiotic (lantibiotic) active on Gram-positive bacteria, such as Lactobacillus sakei, Leuconostoc mesenteroides and Pediococcus pentosaceus. The bactericidal activity of lantibiotics is based on depolarization of energized bacterial cytoplasmic membranes, initiated by the formation of aqueous transmembrane pores.<ref>PMID:16233732</ref> <ref>PMID:16957223</ref> [REFERENCE:4]	+	[https://www.uniprot.org/uniprot/LANNA_STAWA LANNA_STAWA] Lanthionine-containing peptide antibiotic (lantibiotic) active on Gram-positive bacteria, such as Lactobacillus sakei, Leuconostoc mesenteroides and Pediococcus pentosaceus. The bactericidal activity of lantibiotics is based on depolarization of energized bacterial cytoplasmic membranes, initiated by the formation of aqueous transmembrane pores.<ref>PMID:16233732</ref> <ref>PMID:16957223</ref> [REFERENCE:4]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Staphylococcus warneri]]		[[Category: Staphylococcus warneri]]
-	[[Category: Fujinami, D]]	+	[[Category: Fujinami D]]
-	[[Category: Kohda, D]]	+	[[Category: Kohda D]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Lantibiotic~~]]	+

OCA at 21:14, 28 October 2020

OCA — Wed, 28 Oct 2020 21:14:44 GMT

←Older revision		Revision as of 21:14, 28 October 2020
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	==Nukacin ISK-1 in inactive state==		==Nukacin ISK-1 in inactive state==
-	<StructureSection load='5z5r' size='340' side='right' caption='[[5z5r]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5z5r' size='340' side='right'caption='[[5z5r]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z5R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z5R FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene></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=5z5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5r OCA], [http://pdbe.org/5z5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5r RCSB], [http://www.ebi.ac.uk/pdbsum/5z5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5r 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=5z5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5r OCA], [http://pdbe.org/5z5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5r RCSB], [http://www.ebi.ac.uk/pdbsum/5z5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Staphylococcus warneri]]		[[Category: Staphylococcus warneri]]
	[[Category: Fujinami, D]]		[[Category: Fujinami, D]]

OCA at 20:23, 2 December 2018

OCA — Sun, 02 Dec 2018 20:23:19 GMT

←Older revision		Revision as of 20:23, 2 December 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5z5r is ~~ON HOLD until Paper~~ Publication	+	==Nukacin ISK-1 in inactive state==
		+	<StructureSection load='5z5r' size='340' side='right' caption='[[5z5r]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z5r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_warneri Staphylococcus warneri]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5R FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene></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=5z5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5r OCA], [http://pdbe.org/5z5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5r RCSB], [http://www.ebi.ac.uk/pdbsum/5z5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5r ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LANNA_STAWA LANNA_STAWA]] Lanthionine-containing peptide antibiotic (lantibiotic) active on Gram-positive bacteria, such as Lactobacillus sakei, Leuconostoc mesenteroides and Pediococcus pentosaceus. The bactericidal activity of lantibiotics is based on depolarization of energized bacterial cytoplasmic membranes, initiated by the formation of aqueous transmembrane pores.<ref>PMID:16233732</ref> <ref>PMID:16957223</ref> [REFERENCE:4]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The lantibiotic nukacin ISK-1 exerts antimicrobial activity through binding to lipid II. Here, we perform NMR analyses of the structure of nukacin ISK-1 and the interaction with lipid II. Unexpectedly, nukacin ISK-1 exists in two structural states in aqueous solution, with an interconversion rate on a time scale of seconds. The two structures differ in the relative orientations of the two lanthionine rings, ring A and ring C. Chemical shift perturbation induced by the titration of lipid II reveals that only one state was capable of binding to lipid II. On the molecular surface of the active state, a multiple hydrogen-bonding site formed by amino acid residues in the ring A region is adjacent to a hydrophobic surface formed by residues in the ring C region, and we propose that these sites interact with the pyrophosphate moiety and the isoprene chain of the lipid II molecule, respectively.

-	~~Authors: Kohda, D~~., Fujinami, D.	+	The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.,Fujinami D, -Mahin AA, Elsayed KM, Islam MR, Nagao JI, Roy U, Momin S, Zendo T, Kohda D, Sonomoto K Commun Biol. 2018 Sep 25;1:150. doi: 10.1038/s42003-018-0150-3. eCollection 2018. PMID:30272026<ref>PMID:30272026</ref>

-	~~Description: Nukacin ISK-1 in inactive state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Kohda, D~~]]	+	<div class="pdbe-citations 5z5r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Staphylococcus warneri]]
	[[Category: Fujinami, D]]		[[Category: Fujinami, D]]
		+	[[Category: Kohda, D]]
		+	[[Category: Antibiotic]]
		+	[[Category: Lantibiotic]]

OCA at 04:52, 28 February 2018

OCA — Wed, 28 Feb 2018 04:52:13 GMT

←Older revision		Revision as of 04:52, 28 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z5r is ON HOLD	+	The entry 5z5r is ON HOLD until Paper Publication

	Authors: Kohda, D., Fujinami, D.		Authors: Kohda, D., Fujinami, D.

OCA: Protected "5z5r" [edit=sysop:move=sysop]

OCA — Wed, 24 Jan 2018 17:13:04 GMT

Protected "5z5r" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:13, 24 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z5r is ON HOLD Authors: Kohda, D., Fujinami, D. Description: Nukacin ISK-1 in inactive state Category: Unreleased Structures [[Category: Kohda...

OCA — Wed, 24 Jan 2018 17:13:03 GMT

New page: '''Unreleased structure''' The entry 5z5r is ON HOLD Authors: Kohda, D., Fujinami, D. Description: Nukacin ISK-1 in inactive state Category: Unreleased Structures [[Category: Kohda...

New page

'''Unreleased structure'''

The entry 5z5r is ON HOLD

Authors: Kohda, D., Fujinami, D.

Description: Nukacin ISK-1 in inactive state
[[Category: Unreleased Structures]]
[[Category: Kohda, D]]
[[Category: Fujinami, D]]