6r64 - Revision history

OCA at 12:16, 24 January 2024

OCA — Wed, 24 Jan 2024 12:16:01 GMT

←Older revision		Revision as of 12:16, 24 January 2024
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	<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r64]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R64 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r64]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R64 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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]] 2.64Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ghc\|6ghc]]~~, [[~~6t21~~\|~~6t21]], [[6t22\|6t22~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~mcrA, rglA, b1159, JW1145 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=83333 ECOLI])~~</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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [https://pdbe.org/6r64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [https://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [~~http~~://pdbe.org/6r64 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MCRA_ECOLI MCRA_ECOLI]] Restriction of 5-methyl and 5-hydroxymethylcytosines at the specific DNA sequence C(me)CGG.	+	[https://www.uniprot.org/uniprot/MCRA_ECOLI MCRA_ECOLI] Restriction of 5-methyl and 5-hydroxymethylcytosines at the specific DNA sequence C(me)CGG.
	<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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bochtler, M]]	+	[[Category: Synthetic construct]]
-	[[Category: Czapinska, H]]	+	[[Category: Bochtler M]]
-	[[Category: Sasnauskas, G]]	+	[[Category: Czapinska H]]
-	[[Category: Slyvka, A]]	+	[[Category: Sasnauskas G]]
-	[[Category: Zagorskaite, E]]	+	[[Category: Slyvka A]]
-	~~[[Category: 5-hydroxymethylcytosine]]~~	+	[[Category: Zagorskaite E]]
-	~~[[Category: 5-methylcytosine]]~~	+
-	~~[[Category: Bba-me nuclease]]~~	+
-	~~[[Category: Ecokmcra]]~~	+
-	~~[[Category: Hnh endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Modification dependent restriction]]~~	+
-	~~[[Category: N-terminal domain]]~~	+
-	~~[[Category: Neco]]~~	+
-	~~[[Category: Scomcra~~]]	+

OCA at 09:24, 27 November 2019

OCA — Wed, 27 Nov 2019 09:24:20 GMT

←Older revision		Revision as of 09:24, 27 November 2019
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	<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r64]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R64 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r64]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R64 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ghc\|6ghc]], [[6t21\|6t21]], [[6t22\|6t22]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ghc\|6ghc]], [[6t21\|6t21]], [[6t22\|6t22]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mcrA, rglA, b1159, JW1145 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [http://pdbe.org/6r64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [http://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [http://pdbe.org/6r64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [http://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 ProSAT]</span></td></tr>
	</table>		</table>
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Escherichia coli ~~McrA (EcoKMcrA) acts~~ as a ~~methylcytosine and hydroxymethylcytosine dependent restriction endonuclease~~. ~~We present~~ a ~~biochemical characterization of EcoKMcrA~~ that ~~includes the first demonstration of its endonuclease activity, small angle X-ray scattering (SAXS) data~~, and a ~~crystal structure of the enzyme in the absence of DNA. Our data indicate that EcoKMcrA dimerizes via the anticipated~~ C-terminal HNH ~~domains, which together form a single DNA binding site~~. ~~The N~~-~~terminal domains~~ are ~~not homologous~~ to ~~SRA domains~~, ~~do not interact~~ with ~~each other~~, and ~~have separate DNA binding sites~~. ~~Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest that~~ the ~~N-terminal domains can sense~~ the ~~presence~~ and ~~sequence context~~ of ~~modified cytosines~~. ~~Pyrrolocytosine fluorescence data indicate no base flipping. In vitro~~, ~~EcoKMcrA~~ DNA ~~endonuclease activity requires Mn2+ ions, is not strictly~~ methyl ~~dependent, and is not observed when active site variants of the enzyme~~ are ~~used~~. ~~In cells~~, ~~EcoKMcrA specifically restricts DNA that is modified in~~ the ~~correct sequence context. This activity is impaired by mutations~~ of the ~~nuclease active site, unless the enzyme is highly overexpressed~~.	+	EcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N-terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, we report that NEco and full-length EcoKMcrA specificities are consistent. NEco affinity to DNA increases more from hemi- to full-methylation than from non- to hemi-methylation, indicating cooperative binding of the methyl groups. We determined the crystal structures of NEco in complex with fully modified DNA containing three variants of the Y5mCGR EcoKMcrA target sequence: C5mCGG, T5mCGA and T5hmCGA. The structures explain the specificity for the two central base pairs and one of the flanking pairs. As predicted based on earlier biochemical experiments, NEco does not flip any DNA bases. The proximal and distal methyl groups are accommodated in separate pockets. Changes to either pocket reduce DNA binding by NEco and restriction by EcoKMcrA, confirming the relevance of the crystallographically observed binding mode in solution.

-	~~Activity and~~ structure of EcoKMcrA.,~~Czapinska H, Kowalska M~~, Zagorskaite E, ~~Manakova E, Slyvka A, Xu SY, Siksnys V~~, Sasnauskas G, Bochtler M Nucleic Acids Res. ~~2018 Aug 10~~. pii: ~~5068907~~. doi: 10.1093/nar/~~gky731~~. PMID:~~30107581~~<ref>PMID:~~30107581~~</ref>	+	Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.,Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M Nucleic Acids Res. 2019 Nov 14. pii: 5625526. doi: 10.1093/nar/gkz1017. PMID:31724709<ref>PMID:31724709</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bochtler, M]]		[[Category: Bochtler, M]]

OCA at 07:02, 23 October 2019

OCA — Wed, 23 Oct 2019 07:02:11 GMT

←Older revision		Revision as of 07:02, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r64 is ~~ON HOLD~~	+	==N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in complex with C5mCGG target sequence==
		+	<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution\|resolution]] 2.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r64]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R64 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ghc\|6ghc]], [[6t21\|6t21]], [[6t22\|6t22]]</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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [http://pdbe.org/6r64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [http://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MCRA_ECOLI MCRA_ECOLI]] Restriction of 5-methyl and 5-hydroxymethylcytosines at the specific DNA sequence C(me)CGG.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity, small angle X-ray scattering (SAXS) data, and a crystal structure of the enzyme in the absence of DNA. Our data indicate that EcoKMcrA dimerizes via the anticipated C-terminal HNH domains, which together form a single DNA binding site. The N-terminal domains are not homologous to SRA domains, do not interact with each other, and have separate DNA binding sites. Electrophoretic mobility shift assay (EMSA) and footprinting experiments suggest that the N-terminal domains can sense the presence and sequence context of modified cytosines. Pyrrolocytosine fluorescence data indicate no base flipping. In vitro, EcoKMcrA DNA endonuclease activity requires Mn2+ ions, is not strictly methyl dependent, and is not observed when active site variants of the enzyme are used. In cells, EcoKMcrA specifically restricts DNA that is modified in the correct sequence context. This activity is impaired by mutations of the nuclease active site, unless the enzyme is highly overexpressed.

-	~~Authors~~:	+	Activity and structure of EcoKMcrA.,Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M Nucleic Acids Res. 2018 Aug 10. pii: 5068907. doi: 10.1093/nar/gky731. PMID:30107581<ref>PMID:30107581</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r64" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bochtler, M]]
		+	[[Category: Czapinska, H]]
		+	[[Category: Sasnauskas, G]]
		+	[[Category: Slyvka, A]]
		+	[[Category: Zagorskaite, E]]
		+	[[Category: 5-hydroxymethylcytosine]]
		+	[[Category: 5-methylcytosine]]
		+	[[Category: Bba-me nuclease]]
		+	[[Category: Ecokmcra]]
		+	[[Category: Hnh endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Modification dependent restriction]]
		+	[[Category: N-terminal domain]]
		+	[[Category: Neco]]
		+	[[Category: Scomcra]]

OCA: Protected "6r64" [edit=sysop:move=sysop]

OCA — Wed, 03 Apr 2019 05:01:14 GMT

Protected "6r64" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r64 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 03 Apr 2019 05:01:12 GMT

New page: '''Unreleased structure''' The entry 6r64 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r64 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]