6nju - Revision history

OCA at 06:55, 11 October 2023

OCA — Wed, 11 Oct 2023 06:55:06 GMT

←Older revision		Revision as of 06:55, 11 October 2023
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	<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6NJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NJU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.35Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [~~http~~://pdbe.org/6nju PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nju PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju 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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [https://pdbe.org/6nju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [https://www.ebi.ac.uk/pdbsum/6nju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NUCG_MOUSE NUCG_MOUSE]] Cleaves DNA at double-stranded (DG)n.(DC)n and at single-stranded (DC)n tracts. In addition to deoxyribonuclease activities, also has ribonuclease (RNase) and RNase H activities. Capable of generating the RNA primers required by DNA polymerase gamma to initiate replication of mitochondrial DNA (By similarity).	+	[https://www.uniprot.org/uniprot/NUCG_MOUSE NUCG_MOUSE] Cleaves DNA at double-stranded (DG)n.(DC)n and at single-stranded (DC)n tracts. In addition to deoxyribonuclease activities, also has ribonuclease (RNase) and RNase H activities. Capable of generating the RNA primers required by DNA polymerase gamma to initiate replication of mitochondrial DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6nju" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6nju" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Czarny~~, R S~~]]	+	[[Category: Czarny RS]]
-	[[Category: Ho~~, E N~~]]	+	[[Category: Ho EN]]
-	[[Category: Ho~~, P S~~]]	+	[[Category: Ho PS]]
-	[[Category: Robertson~~, A B~~]]	+	[[Category: Robertson AB]]
-	[[Category: Zanden~~, C M.Vander]]~~	+	[[Category: Vander Zanden CM]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Recombination~~]]	+

OCA at 06:02, 22 April 2020

OCA — Wed, 22 Apr 2020 06:02:33 GMT

←Older revision		Revision as of 06:02, 22 April 2020
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	<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6NJU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [http://pdbe.org/6nju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [http://www.ebi.ac.uk/pdbsum/6nju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju 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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [http://pdbe.org/6nju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [http://www.ebi.ac.uk/pdbsum/6nju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:55, 11 March 2020

OCA — Wed, 11 Mar 2020 07:55:12 GMT

←Older revision		Revision as of 07:55, 11 March 2020
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NUCG_MOUSE NUCG_MOUSE]] Cleaves DNA at double-stranded (DG)n.(DC)n and at single-stranded (DC)n tracts. In addition to deoxyribonuclease activities, also has ribonuclease (RNase) and RNase H activities. Capable of generating the RNA primers required by DNA polymerase gamma to initiate replication of mitochondrial DNA (By similarity).		[[http://www.uniprot.org/uniprot/NUCG_MOUSE NUCG_MOUSE]] Cleaves DNA at double-stranded (DG)n.(DC)n and at single-stranded (DC)n tracts. In addition to deoxyribonuclease activities, also has ribonuclease (RNase) and RNase H activities. Capable of generating the RNA primers required by DNA polymerase gamma to initiate replication of mitochondrial DNA (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Modified DNA bases functionally distinguish the taxonomic forms of life-5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an alpha-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C-H < S-H < O-H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.
		+
		+	Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function.,Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS Nucleic Acids Res. 2020 Feb 25. pii: 5755888. doi: 10.1093/nar/gkaa117. PMID:32095813<ref>PMID:32095813</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nju" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:14, 29 January 2020

OCA — Wed, 29 Jan 2020 16:14:27 GMT

←Older revision		Revision as of 16:14, 29 January 2020
Line 3:		Line 3:
	<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endog ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [http://pdbe.org/6nju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [http://www.ebi.ac.uk/pdbsum/6nju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju 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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [http://pdbe.org/6nju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [http://www.ebi.ac.uk/pdbsum/6nju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Czarny, R S]]		[[Category: Czarny, R S]]
	[[Category: Ho, E N]]		[[Category: Ho, E N]]

OCA at 07:34, 8 January 2020

OCA — Wed, 08 Jan 2020 07:34:25 GMT

←Older revision		Revision as of 07:34, 8 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nju ~~is ON HOLD until Paper Publication~~	+	==Mouse endonuclease G mutant H97A bound to A-DNA==
-		+	<StructureSection load='6nju' size='340' side='right'caption='[[6nju]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~Authors~~: ~~Vander Zanden, C~~.M., Ho, E.N., ~~Czarny, R~~.S., ~~Robertson~~, A.B., Ho, P.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nju]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJU FirstGlance]. <br>
-	~~Description~~: ~~Mouse endonuclease G mutant H97A bound to A~~-DNA	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=6nju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nju OCA], [http://pdbe.org/6nju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nju RCSB], [http://www.ebi.ac.uk/pdbsum/6nju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nju ProSAT]</span></td></tr>
-	[[Category: Ho, P.S]]	+	</table>
-	[[Category: ~~Czarny~~, R.S]]	+	== Function ==
-	[[Category: Robertson, A.B]]	+	[[http://www.uniprot.org/uniprot/NUCG_MOUSE NUCG_MOUSE]] Cleaves DNA at double-stranded (DG)n.(DC)n and at single-stranded (DC)n tracts. In addition to deoxyribonuclease activities, also has ribonuclease (RNase) and RNase H activities. Capable of generating the RNA primers required by DNA polymerase gamma to initiate replication of mitochondrial DNA (By similarity).
-	[[Category: ~~Vander~~ Zanden, C.M]]	+	__TOC__
-	[[Category: ~~Ho, E.N~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Czarny, R S]]
		+	[[Category: Ho, E N]]
		+	[[Category: Ho, P S]]
		+	[[Category: Robertson, A B]]
		+	[[Category: Zanden, C M.Vander]]
		+	[[Category: Complex]]
		+	[[Category: Endonuclease]]
		+	[[Category: Recombination]]

OCA at 07:08, 2 October 2019

OCA — Wed, 02 Oct 2019 07:08:49 GMT

←Older revision		Revision as of 07:08, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Vander Zanden, C.M., Ho, E.N., Czarny, R.S., Robertson, A.B., Ho, P.S.		Authors: Vander Zanden, C.M., Ho, E.N., Czarny, R.S., Robertson, A.B., Ho, P.S.

-	Description: Mouse endonuclease G mutant ~~H138A~~ bound to A-DNA	+	Description: Mouse endonuclease G mutant H97A bound to A-DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ho, P.S]]		[[Category: Ho, P.S]]

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

OCA — Wed, 16 Jan 2019 10:39:42 GMT

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

←Older revision

Revision as of 10:39, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nju is ON HOLD Authors: Vander Zanden, C.M., Ho, E.N., Czarny, R.S., Robertson, A.B., Ho, P.S. Description: Mouse endonuclease G mutant H138A boun...

OCA — Wed, 16 Jan 2019 10:39:41 GMT

New page: '''Unreleased structure''' The entry 6nju is ON HOLD Authors: Vander Zanden, C.M., Ho, E.N., Czarny, R.S., Robertson, A.B., Ho, P.S. Description: Mouse endonuclease G mutant H138A boun...

New page

'''Unreleased structure'''

The entry 6nju is ON HOLD

Authors: Vander Zanden, C.M., Ho, E.N., Czarny, R.S., Robertson, A.B., Ho, P.S.

Description: Mouse endonuclease G mutant H138A bound to A-DNA
[[Category: Unreleased Structures]]
[[Category: Ho, P.S]]
[[Category: Czarny, R.S]]
[[Category: Robertson, A.B]]
[[Category: Vander Zanden, C.M]]
[[Category: Ho, E.N]]