4wd9 - Revision history

OCA at 00:52, 28 December 2023

2023-12-28T00:52:40Z

←Older revision		Revision as of 00:52, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WD9 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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [https://pdbe.org/4wd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [https://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></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]] 2.9Å</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [https://pdbe.org/4wd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [https://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:03, 7 April 2023

2023-04-07T07:03:12Z

←Older revision		Revision as of 07:03, 7 April 2023
Line 1:		Line 1:

	==Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide==		==Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide==
-	<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4wd9' size='340' side='right'caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"lactococcus_lactis_subsp~~.~~_diacitilactis_(sic)"_(garvie_and_farrow_1982)_schleifer_et_al._1986 "lactococcus~~ lactis subsp. ~~diacitilactis (sic)" (garvie and farrow 1982) schleifer et al. 1986~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nisB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1360 "Lactococcus lactis subsp. diacitilactis (sic)" (Garvie and Farrow 1982) Schleifer et al. 1986])</td></tr>	+	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [https://pdbe.org/4wd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [https://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [~~http~~://pdbe.org/4wd9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NISB_LACLL NISB_LACLL]] Involved in the post-translational modification of the lantibiotic nisin.	+	[https://www.uniprot.org/uniprot/NISB_LACLL NISB_LACLL] Involved in the post-translational modification of the lantibiotic nisin.
	<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: ~~Hao, Y~~]]	+	[[Category: Lactococcus lactis subsp. lactis]]
-	[[Category: ~~Nair, S K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Biosynthetic protein~~]]	+	[[Category: Hao Y]]
-	[[Category: ~~Class i lantibiotic dehydratase~~]]	+	[[Category: Nair SK]]

OCA at 09:25, 22 November 2017

2017-11-22T09:25:27Z

←Older revision		Revision as of 09:25, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"lactococcus_lactis_subsp._diacitilactis_(sic)"_(garvie_and_farrow_1982)_schleifer_et_al._1986 "lactococcus lactis subsp. diacitilactis (sic)" (garvie and farrow 1982) schleifer et al. 1986]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>
-	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://pdbe.org/4wd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nisB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1360 "Lactococcus lactis subsp. diacitilactis (sic)" (Garvie and Farrow 1982) Schleifer et al. 1986])</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://pdbe.org/4wd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	[[Category: Hao, Y]]		[[Category: Hao, Y]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]
		+	[[Category: Biosynthetic protein]]
	[[Category: Class i lantibiotic dehydratase]]		[[Category: Class i lantibiotic dehydratase]]

OCA at 21:22, 11 August 2016

2016-08-11T21:22:15Z

←Older revision		Revision as of 21:22, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide==		==Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide==
	<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>
-	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>	+	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://pdbe.org/4wd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wd9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4wd9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:46, 25 December 2014

2014-12-25T06:46:52Z

←Older revision		Revision as of 06:46, 25 December 2014
Line 5:		Line 5:
	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>		</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NISB_LACLL NISB_LACLL]] Involved in the post-translational modification of the lantibiotic nisin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:07, 26 November 2014

2014-11-26T06:07:52Z

←Older revision		Revision as of 06:07, 26 November 2014
Line 5:		Line 5:
	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>		</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lantibiotics are a class of peptide antibiotics that contain one or more thioether bonds. The lantibiotic nisin is an antimicrobial peptide that is widely used as a food preservative to combat food-borne pathogens. Nisin contains dehydroalanine and dehydrobutyrine residues that are formed by the dehydration of Ser/Thr by the lantibiotic dehydratase NisB (ref. 2). Recent biochemical studies revealed that NisB glutamylates Ser/Thr side chains as part of the dehydration process. However, the molecular mechanism by which NisB uses glutamate to catalyse dehydration remains unresolved. Here we show that this process involves glutamyl-tRNAGlu to activate Ser/Thr residues. In addition, the 2.9-A crystal structure of NisB in complex with its substrate peptide NisA reveals the presence of two separate domains that catalyse the Ser/Thr glutamylation and glutamate elimination steps. The co-crystal structure also provides insights into substrate recognition by lantibiotic dehydratases. Our findings demonstrate an unexpected role for aminoacyl-tRNA in the formation of dehydroamino acids in lantibiotics, and serve as a basis for the functional characterization of the many lantibiotic-like dehydratases involved in the biosynthesis of other classes of natural products.
		+
		+	Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.,Ortega MA, Hao Y, Zhang Q, Walker MC, van der Donk WA, Nair SK Nature. 2014 Oct 26. doi: 10.1038/nature13888. PMID:25363770<ref>PMID:25363770</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Hao, Y.]]	+	[[Category: Hao, Y]]
-	[[Category: Nair, S K.]]	+	[[Category: Nair, S K]]
	[[Category: Class i lantibiotic dehydratase]]		[[Category: Class i lantibiotic dehydratase]]

OCA at 11:34, 29 October 2014

2014-10-29T11:34:04Z

←Older revision		Revision as of 11:34, 29 October 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide==
-		+	<StructureSection load='4wd9' size='340' side='right' caption='[[4wd9]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~The entry~~ 4wd9 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4wd9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WD9 FirstGlance]. <br>
-	~~Authors~~: Hao, Y., Nair, S.K.	+	</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=4wd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wd9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wd9 RCSB], [http://www.ebi.ac.uk/pdbsum/4wd9 PDBsum]</span></td></tr>
-		+	</table>
-	~~Description~~: ~~Crystal structure of tRNA-dependent~~ lantibiotic dehydratase ~~NisB in complex with NisA leader peptide~~	+	__TOC__
		+	</StructureSection>
		+	[[Category: Hao, Y.]]
		+	[[Category: Nair, S K.]]
		+	[[Category: Class i lantibiotic dehydratase]]

OCA at 09:50, 20 October 2014

2014-10-20T09:50:33Z

←Older revision		Revision as of 09:50, 20 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4wd9 is ON HOLD	+	The entry 4wd9 is ON HOLD until Paper Publication

	Authors: Hao, Y., Nair, S.K.		Authors: Hao, Y., Nair, S.K.

	Description: Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide		Description: Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide

OCA: Protected "4wd9" [edit=sysop:move=sysop]

2014-09-24T09:09:25Z

Protected "4wd9" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:09, 24 September 2014

OCA: New page: '''Unreleased structure''' The entry 4wd9 is ON HOLD Authors: Hao, Y., Nair, S.K. Description: Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA lea...

2014-09-24T09:09:23Z

New page: '''Unreleased structure''' The entry 4wd9 is ON HOLD Authors: Hao, Y., Nair, S.K. Description: Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA lea...

New page

'''Unreleased structure'''

The entry 4wd9 is ON HOLD

Authors: Hao, Y., Nair, S.K.

Description: Crystal structure of tRNA-dependent lantibiotic dehydratase NisB in complex with NisA leader peptide