OCA at 15:16, 18 October 2023

OCA — Wed, 18 Oct 2023 15:16:45 GMT

←Older revision		Revision as of 15:16, 18 October 2023
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-	====	+	==Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU at the active site==
-	<StructureSection load='7k30' size='340' side='right'caption='[[7k30]]' scene=''>	+	<StructureSection load='7k30' size='340' side='right'caption='[[7k30]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7k30]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] 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=7K30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K30 FirstGlance]. <br>
-	</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=7k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k30 OCA], [https://pdbe.org/7k30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k30 RCSB], [https://www.ebi.ac.uk/pdbsum/7k30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k30 ProSAT]</span></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]] 2.34Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k30 OCA], [https://pdbe.org/7k30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k30 RCSB], [https://www.ebi.ac.uk/pdbsum/7k30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k30 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8U0N5_PYRFU Q8U0N5_PYRFU]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Spontaneous deamination of DNA cytosine and adenine into uracil and hypoxanthine, respectively, causes C to T and A to G transition mutations if left unrepaired. Endonuclease Q (EndoQ) initiates the repair of these premutagenic DNA lesions in prokaryotes by cleaving the phosphodiester backbone 5' of either uracil or hypoxanthine bases or an apurinic/apyrimidinic (AP) lesion generated by the excision of these damaged bases. To understand how EndoQ achieves selectivity toward these structurally diverse substrates without cleaving undamaged DNA, we determined the crystal structures of Pyrococcus furiosus EndoQ bound to DNA substrates containing uracil, hypoxanthine, or an AP lesion. The structures show that substrate engagement by EndoQ depends both on a highly distorted conformation of the DNA backbone, in which the target nucleotide is extruded out of the helix, and direct hydrogen bonds with the deaminated bases. A concerted swing motion of the zinc-binding and C-terminal helical domains of EndoQ toward its catalytic domain allows the enzyme to clamp down on a sharply bent DNA substrate, shaping a deep active-site pocket that accommodates the extruded deaminated base. Within this pocket, uracil and hypoxanthine bases interact with distinct sets of amino acid residues, with positioning mediated by an essential magnesium ion. The EndoQ-DNA complex structures reveal a unique mode of damaged DNA recognition and provide mechanistic insights into the initial step of DNA damage repair by the alternative excision repair pathway. Furthermore, we demonstrate that the unique activity of EndoQ is useful for studying DNA deamination and repair in mammalian systems.
		+
		+	Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.,Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2021120118. doi: , 10.1073/pnas.2021120118. PMID:33658373<ref>PMID:33658373</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7k30" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Pyrococcus furiosus]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Aihara H]]
		+	[[Category: Banerjee S]]
		+	[[Category: Moeller NM]]
		+	[[Category: Orellana K]]
		+	[[Category: Shi K]]
		+	[[Category: Yin L]]

OCA at 06:48, 17 March 2021

OCA — Wed, 17 Mar 2021 06:48:02 GMT

←Older revision		Revision as of 06:48, 17 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7k30 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7k30' size='340' side='right'caption='[[7k30]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k30 OCA], [https://pdbe.org/7k30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k30 RCSB], [https://www.ebi.ac.uk/pdbsum/7k30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k30 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 08:40, 17 February 2021

OCA — Wed, 17 Feb 2021 08:40:13 GMT

←Older revision		Revision as of 08:40, 17 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k30 is ON HOLD	+	The entry 7k30 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 09:11, 10 February 2021

OCA — Wed, 10 Feb 2021 09:11:51 GMT

←Older revision		Revision as of 09:11, 10 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7k30 is ON HOLD ~~until Paper Publication~~	+	The entry 7k30 is ON HOLD

	Authors:		Authors:

OCA: Protected "7k30" [edit=sysop:move=sysop]

OCA — Wed, 16 Sep 2020 07:09:03 GMT

Protected "7k30" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:09, 16 September 2020

OCA: New page: '''Unreleased structure''' The entry 7k30 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Sep 2020 07:09:02 GMT

New page: '''Unreleased structure''' The entry 7k30 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page