4glc - Revision history

OCA at 15:49, 14 March 2024

OCA — Thu, 14 Mar 2024 15:49:46 GMT

←Older revision		Revision as of 15:49, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GLC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GLC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</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]] 1.831Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</scene></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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [https://pdbe.org/4glc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [https://www.ebi.ac.uk/pdbsum/4glc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4glc 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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [https://pdbe.org/4glc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [https://www.ebi.ac.uk/pdbsum/4glc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4glc ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it is supposed to serve as an intermediate in DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants of the d(CGCGAATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 or at position 9. The observed resolutions were between 1.42 and 1.99 A. Cytosine modification in all cases influences neither the whole B-DNA double helix structure nor the modified base pair geometry. The additional hydroxyl group of 5-hmC with rotational freedom along the C5-C5A bond is preferentially oriented in the 3' direction. A comparison of thermodynamic properties of the dodecamers shows no effect of 5-mC modification and a sequence-dependent only slight destabilizing effect of 5-hmC modification. Also taking into account the results of a previous functional study [Munzel et al. (2011) (Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Chem. Eur. J., 17, 13782-13788)], we conclude that the 5 position of cytosine is an ideal place to encode epigenetic information. Like this, neither the helical structure nor the thermodynamics are changed, and polymerases cannot distinguish 5-hmC and 5-mC from unmodified cytosine, all these effects are making the former ones non-mutagenic.
-
-	Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.,Renciuk D, Blacque O, Vorlickova M, Spingler B Nucleic Acids Res. 2013 Aug 20. PMID:23963698<ref>PMID:23963698</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4glc" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:03, 26 October 2022

OCA — Wed, 26 Oct 2022 07:03:49 GMT

←Older revision		Revision as of 07:03, 26 October 2022
Line 3:		Line 3:
	<StructureSection load='4glc' size='340' side='right'caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='4glc' size='340' side='right'caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GLC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GLC FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [~~http~~://pdbe.org/4glc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4glc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4glc 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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [https://pdbe.org/4glc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [https://www.ebi.ac.uk/pdbsum/4glc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4glc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Renciuk, D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Spingler, B]]~~	+	[[Category: Renciuk D]]
-	~~[[Category: Vorlickova, M]]~~	+	[[Category: Spingler B]]
-	~~[[Category: 5-hydroxymethyl cytosine~~]]	+	[[Category: Vorlickova M]]
-	[[Category: B~~-dna dodecamer~~]]	+
-	[[Category: ~~Dna]]~~	+
-	~~[[Category: Epigenetic~~]]	+

OCA at 07:42, 27 March 2019

OCA — Wed, 27 Mar 2019 07:42:11 GMT

←Older revision		Revision as of 07:42, 27 March 2019
Line 1:		Line 1:

	==DNA dodecamer containing 5-hydroxymethyl-cytosine==		==DNA dodecamer containing 5-hydroxymethyl-cytosine==
-	<StructureSection load='4glc' size='340' side='right' caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='4glc' size='340' side='right'caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLC FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Renciuk, D]]		[[Category: Renciuk, D]]
	[[Category: Spingler, B]]		[[Category: Spingler, B]]

OCA at 16:08, 5 August 2016

OCA — Fri, 05 Aug 2016 16:08:02 GMT

←Older revision		Revision as of 16:08, 5 August 2016
Line 1:		Line 1:
		+
	==DNA dodecamer containing 5-hydroxymethyl-cytosine==		==DNA dodecamer containing 5-hydroxymethyl-cytosine==
	<StructureSection load='4glc' size='340' side='right' caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='4glc' size='340' side='right' caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLC FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</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=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [http://www.ebi.ac.uk/pdbsum/4glc PDBsum]</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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [http://pdbe.org/4glc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [http://www.ebi.ac.uk/pdbsum/4glc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4glc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4glc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:09, 21 December 2014

OCA — Sun, 21 Dec 2014 11:09:25 GMT

←Older revision		Revision as of 11:09, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4glc~~\| ~~PDB~~=4glc \| ~~SCENE~~= }}	+	==DNA dodecamer containing 5-hydroxymethyl-cytosine==
-	===DNA dodecamer containing 5-~~hydroxymethyl~~-cytosine~~===~~	+	<StructureSection load='4glc' size='340' side='right' caption='[[4glc]], [[Resolution\|resolution]] 1.83Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23963698}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLC FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</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=4glc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4glc RCSB], [http://www.ebi.ac.uk/pdbsum/4glc PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	5-Hydroxymethylcytosine (5-hmC) was recently identified as a relatively frequent base in eukaryotic genomes. Its physiological function is still unclear, but it is supposed to serve as an intermediate in DNA de novo demethylation. Using X-ray diffraction, we solved five structures of four variants of the d(CGCGAATTCGCG) dodecamer, containing either 5-hmC or 5-methylcytosine (5-mC) at position 3 or at position 9. The observed resolutions were between 1.42 and 1.99 A. Cytosine modification in all cases influences neither the whole B-DNA double helix structure nor the modified base pair geometry. The additional hydroxyl group of 5-hmC with rotational freedom along the C5-C5A bond is preferentially oriented in the 3' direction. A comparison of thermodynamic properties of the dodecamers shows no effect of 5-mC modification and a sequence-dependent only slight destabilizing effect of 5-hmC modification. Also taking into account the results of a previous functional study [Munzel et al. (2011) (Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Chem. Eur. J., 17, 13782-13788)], we conclude that the 5 position of cytosine is an ideal place to encode epigenetic information. Like this, neither the helical structure nor the thermodynamics are changed, and polymerases cannot distinguish 5-hmC and 5-mC from unmodified cytosine, all these effects are making the former ones non-mutagenic.

-	~~==About this Structure==~~	+	Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.,Renciuk D, Blacque O, Vorlickova M, Spingler B Nucleic Acids Res. 2013 Aug 20. PMID:23963698<ref>PMID:23963698</ref>
-	~~[[4glc]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4GLC OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023963698</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Renciuk, D.]]	+	== References ==
-	[[Category: Spingler, B.]]	+	<references/>
-	[[Category: Vorlickova, M.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Renciuk, D]]
		+	[[Category: Spingler, B]]
		+	[[Category: Vorlickova, M]]
	[[Category: 5-hydroxymethyl cytosine]]		[[Category: 5-hydroxymethyl cytosine]]
	[[Category: B-dna dodecamer]]		[[Category: B-dna dodecamer]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Epigenetic]]		[[Category: Epigenetic]]

OCA at 09:09, 4 September 2013

OCA — Wed, 04 Sep 2013 09:09:33 GMT

←Older revision		Revision as of 09:09, 4 September 2013
Line 1:		Line 1:
	{{STRUCTURE_4glc\| PDB=4glc \| SCENE= }}		{{STRUCTURE_4glc\| PDB=4glc \| SCENE= }}
	===DNA dodecamer containing 5-hydroxymethyl-cytosine===		===DNA dodecamer containing 5-hydroxymethyl-cytosine===
		+	{{ABSTRACT_PUBMED_23963698}}

	==About this Structure==		==About this Structure==
	[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA].		[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023963698</ref><references group="xtra"/><references/>
	[[Category: Renciuk, D.]]		[[Category: Renciuk, D.]]
	[[Category: Spingler, B.]]		[[Category: Spingler, B.]]

OCA at 07:36, 28 August 2013

OCA — Wed, 28 Aug 2013 07:36:32 GMT

←Older revision		Revision as of 07:36, 28 August 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4glc\| PDB=4glc \| SCENE= }}
		+	===DNA dodecamer containing 5-hydroxymethyl-cytosine===

-	~~The entry~~ 4glc is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4glc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLC OCA].
-	~~Authors~~: ~~Spingler, B~~., Renciuk, D., Vorlickova, M.	+	[[Category: Renciuk, D.]]
-		+	[[Category: Spingler, B.]]
-	~~Description~~: ~~DNA dodecamer containing~~ 5-hydroxymethyl-cytosine	+	[[Category: Vorlickova, M.]]
		+	[[Category: 5-hydroxymethyl cytosine]]
		+	[[Category: B-dna dodecamer]]
		+	[[Category: Dna]]
		+	[[Category: Epigenetic]]

OCA at 06:30, 17 October 2012

OCA — Wed, 17 Oct 2012 06:30:54 GMT

←Older revision		Revision as of 06:30, 17 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Spingler, B., Renciuk, D., Vorlickova, M.		Authors: Spingler, B., Renciuk, D., Vorlickova, M.

	Description: DNA dodecamer containing 5-hydroxymethyl-cytosine		Description: DNA dodecamer containing 5-hydroxymethyl-cytosine

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

OCA — Wed, 22 Aug 2012 05:36:41 GMT

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

←Older revision

Revision as of 05:36, 22 August 2012

OCA: New page: '''Unreleased structure''' The entry 4glc is ON HOLD Authors: Spingler, B., Renciuk, D., Vorlickova, M. Description: DNA dodecamer containing 5-hydroxymethyl-cytosine

OCA — Wed, 22 Aug 2012 05:36:40 GMT

New page: '''Unreleased structure''' The entry 4glc is ON HOLD Authors: Spingler, B., Renciuk, D., Vorlickova, M. Description: DNA dodecamer containing 5-hydroxymethyl-cytosine

New page

'''Unreleased structure'''

The entry 4glc is ON HOLD

Authors: Spingler, B., Renciuk, D., Vorlickova, M.

Description: DNA dodecamer containing 5-hydroxymethyl-cytosine