5z3n - Revision history

OCA at 08:44, 22 November 2023

OCA — Wed, 22 Nov 2023 08:44:44 GMT

←Older revision		Revision as of 08:44, 22 November 2023
Line 1:		Line 1:

	==Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA==		==Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA==
-	<StructureSection load='5z3n' size='340' side='right' caption='[[5z3n]], [[Resolution\|resolution]] 1.91Å' scene=''>	+	<StructureSection load='5z3n' size='340' side='right'caption='[[5z3n]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z3n]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z3N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z3n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] 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=5Z3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=DGT:2~~-~~DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.91Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene>, <scene name='pdbligand=~~DOC~~:2,3-~~DIDEOXYCYTIDINE~~-5-~~MONOPHOSPHATE~~'>~~DOC~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">polA~~, ~~pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=271 ATCC 25104])</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=5z3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3n OCA], [https://pdbe.org/5z3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3n RCSB], [https://www.ebi.ac.uk/pdbsum/5z3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3n ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=5z3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3n OCA], [~~http~~://pdbe.org/5z3n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z3n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z3n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3n ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5z3n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5z3n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 25104~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Gao~~, Y Q~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: Mondal, M]]	+	[[Category: Gao YQ]]
-	[[Category: Song~~, R Y~~]]	+	[[Category: Mondal M]]
-	[[Category: Xia, B]]	+	[[Category: Song RY]]
-	[[Category: Yi~~, C Q~~]]	+	[[Category: Xia B]]
-	[[Category: Zeng, H]]	+	[[Category: Yi CQ]]
-	[[Category: Zhang, J]]	+	[[Category: Zeng H]]
-	~~[[Category: Dna]]~~	+	[[Category: Zhang J]]
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Replication-dna complex~~]]	+

OCA at 06:16, 2 January 2019

OCA — Wed, 02 Jan 2019 06:16:18 GMT

←Older revision		Revision as of 06:16, 2 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z3n is ~~ON HOLD~~	+	==Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA==
		+	<StructureSection load='5z3n' size='340' side='right' caption='[[5z3n]], [[Resolution\|resolution]] 1.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z3n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z3N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5z3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3n OCA], [http://pdbe.org/5z3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z3n RCSB], [http://www.ebi.ac.uk/pdbsum/5z3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3n ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which DNA polymerases faithfully decode chemical information on the template. It was previously shown that two unnatural cytosine bases (termed "M-fC" and "I-fC"), which are chemical labeling adducts of the epigenetic base 5-formylcytosine, can induce C-to-T transition during DNA amplification. However, how DNA polymerases recognize such unnatural cytosine bases remains enigmatic. Herein, crystal structures of unnatural cytosine bases pairing to dA/dG in the KlenTaq polymerase-host-guest complex system and pairing to dATP in the KlenTaq polymerase active site were determined. Both M-fC and I-fC base pair with dA/dATP, but not with dG, in a Watson-Crick geometry. This study reveals that the formation of the Watson-Crick geometry, which may be enabled by the A-rule, is important for the recognition of unnatural cytosines.

-	~~Authors:~~ Zeng, H., Mondal, M., Song, R~~.Y.~~, Zhang, J., Xia, B., Gao~~, Y.Q.~~, Yi, C.Q.	+	Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.,Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C Angew Chem Int Ed Engl. 2019 Jan 2;58(1):130-133. doi: 10.1002/anie.201807845., Epub 2018 Dec 5. PMID:30407705<ref>PMID:30407705</ref>

-	~~Description: Structure~~ of ~~large fragment~~ of ~~DNA Polymerase I from Thermus aquaticus Host~~-~~Guest complex with the unnatural base 5fC pair with dA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Song~~, R.Y]]	+	<div class="pdbe-citations 5z3n" style="background-color:#fffaf0;"></div>
-	[[Category: Yi, ~~C.Q~~]]	+	== References ==
-	[[Category: ~~Gao~~, Y.Q]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 25104]]
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Gao, Y Q]]
		+	[[Category: Mondal, M]]
		+	[[Category: Song, R Y]]
	[[Category: Xia, B]]		[[Category: Xia, B]]
-	[[Category: ~~Zhang~~, J]]	+	[[Category: Yi, C Q]]
	[[Category: Zeng, H]]		[[Category: Zeng, H]]
-	[[Category: ~~Mondal~~, M]]	+	[[Category: Zhang, J]]
		+	[[Category: Dna]]
		+	[[Category: Replication]]
		+	[[Category: Replication-dna complex]]

OCA at 17:10, 24 January 2018

OCA — Wed, 24 Jan 2018 17:10:50 GMT

←Older revision		Revision as of 17:10, 24 January 2018
Line 5:		Line 5:
	Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q.		Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q.

-	Description: Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA.	+	Description: Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Song, R.Y]]
		+	[[Category: Yi, C.Q]]
	[[Category: Gao, Y.Q]]		[[Category: Gao, Y.Q]]
	[[Category: Xia, B]]		[[Category: Xia, B]]
		+	[[Category: Zhang, J]]
	[[Category: Zeng, H]]		[[Category: Zeng, H]]
	[[Category: Mondal, M]]		[[Category: Mondal, M]]
-	[[Category: Song, R.Y]]
-	[[Category: Yi, C.Q]]
-	[[Category: Zhang, J]]

OCA: Protected "5z3n" [edit=sysop:move=sysop]

OCA — Wed, 17 Jan 2018 05:32:55 GMT

Protected "5z3n" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 17 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z3n is ON HOLD Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q. Description: Structure of large fragment of DNA ...

OCA — Wed, 17 Jan 2018 05:32:54 GMT

New page: '''Unreleased structure''' The entry 5z3n is ON HOLD Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q. Description: Structure of large fragment of DNA ...

New page

'''Unreleased structure'''

The entry 5z3n is ON HOLD

Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q.

Description: Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA.
[[Category: Unreleased Structures]]
[[Category: Gao, Y.Q]]
[[Category: Xia, B]]
[[Category: Zeng, H]]
[[Category: Mondal, M]]
[[Category: Song, R.Y]]
[[Category: Yi, C.Q]]
[[Category: Zhang, J]]