6k0w - Revision history

OCA at 10:40, 27 March 2024

OCA — Wed, 27 Mar 2024 10:40:43 GMT

←Older revision		Revision as of 10:40, 27 March 2024
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	<StructureSection load='6k0w' size='340' side='right'caption='[[6k0w]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6k0w' size='340' side='right'caption='[[6k0w]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0w]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Campylobacter_pylori Campylobacter~~ pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K0W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SFG:SINEFUNGIN'>SFG</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]] 2.65Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HP_0593 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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=6k0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0w OCA], [~~http~~://pdbe.org/6k0w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k0w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k0w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0w 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=6k0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0w OCA], [https://pdbe.org/6k0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0w RCSB], [https://www.ebi.ac.uk/pdbsum/6k0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0w ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/O25315_HELPY O25315_HELPY]
-	Methylation of genomic DNA can influence the transcription profile of an organism and may generate phenotypic diversity for rapid adaptation in a dynamic environment. M.HpyAXI is a Type III DNA methyltransferase present in Helicobacter pylori and is upregulated at low pH. This enzyme may alter the expression of critical genes to ensure the survival of this pathogen at low pH inside the human stomach. M.HpyAXI methylates the adenine in the target sequence (5'-GCAG-3') and shows maximal activity at pH 5.5. Type III DNA methyltransferases are found to form an inverted dimer in the functional form. We observe that M.HpyAXI forms a nonfunctional dimer at pH 8.0 that is incapable of DNA binding and methylation activity. However, at pH 5.5, two such dimers associate to form a tetramer that now includes two functional dimers that can bind and methylate the target DNA sequence. Overall, we observe that the pH-dependent tetramerization of M.HpyAXI ensures that the enzyme is licensed to act only in the presence of acid stress.	+
-		+
-	Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress.,Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT J Mol Biol. 2019 Oct 16. pii: ~~S0022-2836(19)30579-0. doi:, 10.1016~~/~~j.jmb.2019.10.001. PMID:31628946<ref>PMID:31628946<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6k0w" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Campylobacter~~ pylori]]	+	[[Category: Helicobacter pylori 26695]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nair~~, D T~~]]	+	[[Category: Nair DT]]
-	[[Category: Narayanan, N]]	+	[[Category: Narayanan N]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna methyltransferase]]~~	+
-	~~[[Category: Sinefungin~~]]	+

OCA at 04:37, 13 February 2020

OCA — Thu, 13 Feb 2020 04:37:39 GMT

←Older revision		Revision as of 04:37, 13 February 2020
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	<StructureSection load='6k0w' size='340' side='right'caption='[[6k0w]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6k0w' size='340' side='right'caption='[[6k0w]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0w]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HP_0593 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=6k0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0w OCA], [http://pdbe.org/6k0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0w RCSB], [http://www.ebi.ac.uk/pdbsum/6k0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0w 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=6k0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0w OCA], [http://pdbe.org/6k0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0w RCSB], [http://www.ebi.ac.uk/pdbsum/6k0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0w ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Nair, D T]]		[[Category: Nair, D T]]

OCA at 15:05, 11 December 2019

OCA — Wed, 11 Dec 2019 15:05:33 GMT

←Older revision		Revision as of 15:05, 11 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6k0w is ~~ON HOLD until Paper~~ Publication	+	==DNA methyltransferase in complex with sinefungin==
		+	<StructureSection load='6k0w' size='340' side='right'caption='[[6k0w]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6k0w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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=6k0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0w OCA], [http://pdbe.org/6k0w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0w RCSB], [http://www.ebi.ac.uk/pdbsum/6k0w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methylation of genomic DNA can influence the transcription profile of an organism and may generate phenotypic diversity for rapid adaptation in a dynamic environment. M.HpyAXI is a Type III DNA methyltransferase present in Helicobacter pylori and is upregulated at low pH. This enzyme may alter the expression of critical genes to ensure the survival of this pathogen at low pH inside the human stomach. M.HpyAXI methylates the adenine in the target sequence (5'-GCAG-3') and shows maximal activity at pH 5.5. Type III DNA methyltransferases are found to form an inverted dimer in the functional form. We observe that M.HpyAXI forms a nonfunctional dimer at pH 8.0 that is incapable of DNA binding and methylation activity. However, at pH 5.5, two such dimers associate to form a tetramer that now includes two functional dimers that can bind and methylate the target DNA sequence. Overall, we observe that the pH-dependent tetramerization of M.HpyAXI ensures that the enzyme is licensed to act only in the presence of acid stress.

-	~~Authors: Narayanan~~, N., ~~Nair~~, D.T.	+	Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress.,Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT J Mol Biol. 2019 Oct 16. pii: S0022-2836(19)30579-0. doi:, 10.1016/j.jmb.2019.10.001. PMID:31628946<ref>PMID:31628946</ref>

-	~~Description~~: ~~DNA methyltransferase in complex with sinefungin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Nair, D.T]]	+	<div class="pdbe-citations 6k0w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nair, D T]]
	[[Category: Narayanan, N]]		[[Category: Narayanan, N]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna methyltransferase]]
		+	[[Category: Sinefungin]]

OCA at 04:56, 6 November 2019

OCA — Wed, 06 Nov 2019 04:56:29 GMT

←Older revision		Revision as of 04:56, 6 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k0w is ON HOLD	+	The entry 6k0w is ON HOLD until Paper Publication

	Authors: Narayanan, N., Nair, D.T.		Authors: Narayanan, N., Nair, D.T.

OCA: Protected "6k0w" [edit=sysop:move=sysop]

OCA — Tue, 21 May 2019 05:40:27 GMT

Protected "6k0w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k0w is ON HOLD Authors: Narayanan, N., Nair, D.T. Description: DNA methyltransferase in complex with sinefungin [[Category: Unreleased Structures]...

OCA — Tue, 21 May 2019 05:40:25 GMT

New page: '''Unreleased structure''' The entry 6k0w is ON HOLD Authors: Narayanan, N., Nair, D.T. Description: DNA methyltransferase in complex with sinefungin [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 6k0w is ON HOLD

Authors: Narayanan, N., Nair, D.T.

Description: DNA methyltransferase in complex with sinefungin
[[Category: Unreleased Structures]]
[[Category: Nair, D.T]]
[[Category: Narayanan, N]]