6p0g - Revision history

OCA at 13:07, 25 December 2019

OCA — Wed, 25 Dec 2019 13:07:07 GMT

←Older revision		Revision as of 13:07, 25 December 2019
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	<StructureSection load='6p0g' size='340' side='right'caption='[[6p0g]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='6p0g' size='340' side='right'caption='[[6p0g]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p0g]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p0g]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thegj Thegj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0G FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TGAM_0453 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=593117 THEGJ])</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=6p0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0g OCA], [http://pdbe.org/6p0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0g RCSB], [http://www.ebi.ac.uk/pdbsum/6p0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0g 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=6p0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0g OCA], [http://pdbe.org/6p0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0g RCSB], [http://www.ebi.ac.uk/pdbsum/6p0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The sidechains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA binding domain (Tg185) both alone and in complex with a methylated DNA substrate at 1.68 A and 2.27 A resolution respectively. The structures reveal that Tg185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA binding domain. Structural superposition and co-crystallization further show that Tg185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines while an extended basic surface present in Tg185 facilitates its preferential binding to duplex DNA rather than RNA. Together these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.
		+
		+	The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.,Hosford CJ, Bui AQ, Chappie JS J Biol Chem. 2019 Dec 10. pii: RA119.010188. doi: 10.1074/jbc.RA119.010188. PMID:31822563<ref>PMID:31822563</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p0g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thegj]]
	[[Category: Chappie, J S]]		[[Category: Chappie, J S]]
	[[Category: Hosford, C J]]		[[Category: Hosford, C J]]

OCA at 07:45, 18 December 2019

OCA — Wed, 18 Dec 2019 07:45:04 GMT

←Older revision		Revision as of 07:45, 18 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6p0g is ~~ON HOLD until Paper Publication~~	+	==N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA==
-		+	<StructureSection load='6p0g' size='340' side='right'caption='[[6p0g]], [[Resolution\|resolution]] 2.27Å' scene=''>
-	~~Authors~~: ~~Hosford~~, C.J., ~~Chappie~~, J.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p0g]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0G FirstGlance]. <br>
-	~~Description~~: N-~~terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA~~	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6p0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0g OCA], [http://pdbe.org/6p0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0g RCSB], [http://www.ebi.ac.uk/pdbsum/6p0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0g ProSAT]</span></td></tr>
-	[[Category: ~~Hosford~~, C.J]]	+	</table>
-	[[Category: ~~Chappie~~, J.S]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chappie, J S]]
		+	[[Category: Hosford, C J]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Restriction endonuclease]]
		+	[[Category: Yth domain]]

OCA at 05:11, 26 June 2019

OCA — Wed, 26 Jun 2019 05:11:05 GMT

←Older revision		Revision as of 05:11, 26 June 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p0g is ON HOLD	+	The entry 6p0g is ON HOLD until Paper Publication

	Authors: Hosford, C.J., Chappie, J.S.		Authors: Hosford, C.J., Chappie, J.S.

OCA: Protected "6p0g" [edit=sysop:move=sysop]

OCA — Wed, 29 May 2019 04:32:55 GMT

Protected "6p0g" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:32, 29 May 2019

OCA: New page: '''Unreleased structure''' The entry 6p0g is ON HOLD Authors: Hosford, C.J., Chappie, J.S. Description: N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA [[Category...

OCA — Wed, 29 May 2019 04:32:53 GMT

New page: '''Unreleased structure''' The entry 6p0g is ON HOLD Authors: Hosford, C.J., Chappie, J.S. Description: N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA [[Category...

New page

'''Unreleased structure'''

The entry 6p0g is ON HOLD

Authors: Hosford, C.J., Chappie, J.S.

Description: N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA
[[Category: Unreleased Structures]]
[[Category: Hosford, C.J]]
[[Category: Chappie, J.S]]