6nkl - Revision history

OCA at 06:55, 11 October 2023

OCA — Wed, 11 Oct 2023 06:55:23 GMT

←Older revision		Revision as of 06:55, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium~~ influenzae~~" lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6NKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NKL FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~727~~ "~~Bacterium influenzae~~" ~~Lehmann and Neumann 1896])~~, ~~vapB1, BV136_01366, BVZ80_01199, CH628_04350 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])~~</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]] 2.2Å</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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [~~http~~://pdbe.org/6nkl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl 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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [https://pdbe.org/6nkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [https://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A2R3FUY7_HAEIF A0A2R3FUY7_HAEIF]~~] Toxic component of a toxin-antitoxin (TA) system. An RNase.[~~HAMAP-Rule~~:~~MF_00265~~]	+	[https://www.uniprot.org/uniprot/VAPC1_HAEIN VAPC1_HAEIN] Toxic component of a type II toxin-antitoxin (TA) system. Acts as an RNase, its toxic effect is neutralized by VapB1 antitoxin (By similarity).[UniProtKB:Q4QNL7]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ influenzae ~~lehmann and neumann 1896~~]]	+	[[Category: Haemophilus influenzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Battaile~~, K P~~]]	+	[[Category: Battaile KP]]
-	[[Category: Daines~~, D A~~]]	+	[[Category: Daines DA]]
-	[[Category: Kashipathy~~, M M~~]]	+	[[Category: Kashipathy MM]]
-	[[Category: Lovell, S]]	+	[[Category: Lovell S]]
-	[[Category: Molinaro~~, A L]]~~	+	[[Category: Molinaro AL]]
-	~~[[Category: Antitoxin]]~~	+
-	~~[[Category: H. influenzae]]~~	+
-	~~[[Category: Protein-protein complex]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 06:29, 6 May 2020

OCA — Wed, 06 May 2020 06:29:24 GMT

←Older revision		Revision as of 06:29, 6 May 2020
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	<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6NKL FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896]), vapB1, BV136_01366, BVZ80_01199, CH628_04350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896]), vapB1, BV136_01366, BVZ80_01199, CH628_04350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [http://pdbe.org/6nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [http://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl 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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [http://pdbe.org/6nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [http://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	[[Category: Battaile, K P]]		[[Category: Battaile, K P]]
	[[Category: Daines, D A]]		[[Category: Daines, D A]]
-	[[Category: Kashipathy, M K]]	+	[[Category: Kashipathy, M M]]
	[[Category: Lovell, S]]		[[Category: Lovell, S]]
	[[Category: Molinaro, A L]]		[[Category: Molinaro, A L]]

OCA at 11:35, 18 December 2019

OCA — Wed, 18 Dec 2019 11:35:52 GMT

←Older revision		Revision as of 11:35, 18 December 2019
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6nkl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6nkl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:08, 5 June 2019

OCA — Wed, 05 Jun 2019 23:08:49 GMT

←Older revision		Revision as of 23:08, 5 June 2019
Line 3:		Line 3:
	<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NKL 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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [http://pdbe.org/6nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [http://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896]), vapB1, BV136_01366, BVZ80_01199, CH628_04350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [http://pdbe.org/6nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [http://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Battaile, K P]]		[[Category: Battaile, K P]]

OCA at 07:28, 10 April 2019

OCA — Wed, 10 Apr 2019 07:28:04 GMT

←Older revision		Revision as of 07:28, 10 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nkl is ~~ON HOLD until Paper~~ Publication	+	==2.2 A resolution structure of VapBC-1 from nontypeable Haemophilus influenzae==
		+	<StructureSection load='6nkl' size='340' side='right'caption='[[6nkl]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6nkl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NKL 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=6nkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nkl OCA], [http://pdbe.org/6nkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nkl RCSB], [http://www.ebi.ac.uk/pdbsum/6nkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nkl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A2R3FUY7_HAEIF A0A2R3FUY7_HAEIF]] Toxic component of a toxin-antitoxin (TA) system. An RNase.[HAMAP-Rule:MF_00265]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminus (PIN) domain containing conserved amino acids considered essential for activity. The vapBC (virulence associated protein) TA system is the largest subfamily in this class, and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 A resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi DeltavapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo IMPORTANCE: Herein the crystal structure of the VapBC-1 complex from nontypeable Haemophilus influenzae (NTHi) is described. Our results show that some of the mutations in the PIN domain of the VapC-1 toxin were associated with decreased toxicity in E. coli, but the mutants retained the ability to homodimerize and to heterodimerize with the wild-type cognate antitoxin, VapB-1. A new system was designed and constructed to quantify the effects of these mutations on NTHi survival during infections of primary human tissues ex vivo Any mutation to a conserved amino acid in the PIN domain significantly decreased the number of survivors compared to the in cis wild-type toxin under the same conditions.

-	~~Authors: Lovell, S~~., Kashipathy, ~~M.K.~~, Battaile, ~~K.P.~~, ~~Molinaro~~, A.L.~~, Daines, D~~.A.	+	Crystal structure of VapBC-1 from nontypeable Haemophilus influenzae and the effect of PIN domain mutations on survival during infection.,Molinaro AL, Kashipathy MM, Lovell S, Battaile KP, Coussens NP, Shen M, Daines DA J Bacteriol. 2019 Apr 1. pii: JB.00026-19. doi: 10.1128/JB.00026-19. PMID:30936373<ref>PMID:30936373</ref>

-	~~Description: 2~~.~~2 A resolution structure~~ of ~~VapBC~~-~~1 from nontypeable Haemophilus influenzae~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Battaile, K.P]]	+	<div class="pdbe-citations 6nkl" style="background-color:#fffaf0;"></div>
-	[[Category: Kashipathy, M.K]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Battaile, K P]]
		+	[[Category: Daines, D A]]
		+	[[Category: Kashipathy, M K]]
	[[Category: Lovell, S]]		[[Category: Lovell, S]]
-	[[Category: ~~Daines~~, D.A]]	+	[[Category: Molinaro, A L]]
-	[[Category: ~~Molinaro, A~~.L]]	+	[[Category: Antitoxin]]
		+	[[Category: H. influenzae]]
		+	[[Category: Protein-protein complex]]
		+	[[Category: Toxin]]

OCA at 06:33, 30 January 2019

OCA — Wed, 30 Jan 2019 06:33:32 GMT

←Older revision		Revision as of 06:33, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nkl is ON HOLD	+	The entry 6nkl is ON HOLD until Paper Publication

	Authors: Lovell, S., Kashipathy, M.K., Battaile, K.P., Molinaro, A.L., Daines, D.A.		Authors: Lovell, S., Kashipathy, M.K., Battaile, K.P., Molinaro, A.L., Daines, D.A.
Line 9:		Line 9:
	[[Category: Battaile, K.P]]		[[Category: Battaile, K.P]]
	[[Category: Kashipathy, M.K]]		[[Category: Kashipathy, M.K]]
-	[[Category: Daines, D.A]]
	[[Category: Lovell, S]]		[[Category: Lovell, S]]
		+	[[Category: Daines, D.A]]
	[[Category: Molinaro, A.L]]		[[Category: Molinaro, A.L]]

OCA: Protected "6nkl" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2019 10:42:09 GMT

Protected "6nkl" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:42, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nkl is ON HOLD Authors: Lovell, S., Kashipathy, M.K., Battaile, K.P., Molinaro, A.L., Daines, D.A. Description: 2.2 A resolution structure of VapB...

OCA — Wed, 16 Jan 2019 10:42:07 GMT

New page: '''Unreleased structure''' The entry 6nkl is ON HOLD Authors: Lovell, S., Kashipathy, M.K., Battaile, K.P., Molinaro, A.L., Daines, D.A. Description: 2.2 A resolution structure of VapB...

New page

'''Unreleased structure'''

The entry 6nkl is ON HOLD

Authors: Lovell, S., Kashipathy, M.K., Battaile, K.P., Molinaro, A.L., Daines, D.A.

Description: 2.2 A resolution structure of VapBC-1 from nontypeable Haemophilus influenzae
[[Category: Unreleased Structures]]
[[Category: Battaile, K.P]]
[[Category: Kashipathy, M.K]]
[[Category: Daines, D.A]]
[[Category: Lovell, S]]
[[Category: Molinaro, A.L]]