6lwc - Revision history

OCA at 14:59, 29 November 2023

2023-11-29T14:59:25Z

←Older revision		Revision as of 14:59, 29 November 2023
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-	====	+	==Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)==
-	<StructureSection load='6lwc' size='340' side='right'caption='[[6lwc]]' scene=''>	+	<StructureSection load='6lwc' size='340' side='right'caption='[[6lwc]], [[Resolution\|resolution]] 2.91Å' 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'>[[6lwc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LWC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LWC 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=6lwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lwc OCA], [https://pdbe.org/6lwc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lwc RCSB], [https://www.ebi.ac.uk/pdbsum/6lwc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lwc 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]] 2.91Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EWC:[(2~{R},3~{S},5~{R})-5-[(5~{S})-7-azanyl-2,4,9-tris(oxidanylidene)-1,3,6,8-tetrazaspiro[4.4]non-7-en-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>EWC</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=6lwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lwc OCA], [https://pdbe.org/6lwc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lwc RCSB], [https://www.ebi.ac.uk/pdbsum/6lwc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lwc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NEIL1_HUMAN NEIL1_HUMAN] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, formamidopyrimidine (Fapy) and 5-hydroxyuracil. Has marginal activity towards 8-oxoguanine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Has DNA glycosylase/lyase activity towards mismatched uracil and thymine, in particular in U:C and T:C mismatches.<ref>PMID:12200441</ref> <ref>PMID:12509226</ref> <ref>PMID:11904416</ref> <ref>PMID:14522990</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA glycosylases must distinguish the sparse damaged sites from the vast expanse of normal DNA bases. However, our understanding of the nature of nucleobase interrogation is still limited. Here, we show that hNEIL1 (human endonuclease VIII-like 1) captures base lesions via two competing states of interaction: an activated state that commits catalysis and base excision repair, and a quarantine state that temporarily separates and protects the flipped base via auto-inhibition. The relative dominance of the two states depends on key residues of hNEIL1 and chemical properties (e.g. aromaticity and hydrophilicity) of flipped bases. Such a DNA repair mechanism allows hNEIL1 to recognize a broad spectrum of DNA damage while keeps potential gratuitous repair in check. We further reveal the molecular basis of hNEIL1 activity regulation mediated by post-transcriptional modifications and provide an example of how exquisite structural dynamics serves for orchestrated enzyme functions.
		+
		+	DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes.,Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C Nat Commun. 2021 Jul 5;12(1):4108. doi: 10.1038/s41467-021-24431-y. PMID:34226550<ref>PMID:34226550</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lwc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Gao YQ]]
		+	[[Category: Liu MH]]
		+	[[Category: Yi CQ]]
		+	[[Category: Zhang J]]
		+	[[Category: Zhang XX]]
		+	[[Category: Zhu CX]]

OCA at 12:08, 9 June 2021

2021-06-09T12:08:50Z

←Older revision		Revision as of 12:08, 9 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6lwc ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6lwc' size='340' side='right'caption='[[6lwc]]' scene=''>
-	~~Authors~~: ~~Liu, M~~.H.~~, Zhang, J~~.~~, Zhu, C~~.X.~~, Zhang, X~~.X.~~, Gao, Y~~.Q., ~~Yi, C~~.Q.	+	== 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: Crystal structure of human NEIL1(P2G~~, ~~E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)~~	+	</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=6lwc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lwc OCA], [https://pdbe.org/6lwc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lwc RCSB], [https://www.ebi.ac.uk/pdbsum/6lwc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lwc ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Zhu, C~~.X]]	+	__TOC__
-	[~~[Category~~: ~~Gao, Y~~.Q]]	+	</StructureSection>
-	~~[[Category: Zhang~~, ~~J]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Zhang, X~~.X]]	+	[[Category: Z-disk]]
-	[[Category: ~~Liu, M.H~~]]	+
-	[[Category: ~~Yi, C.Q~~]]	+

OCA at 05:29, 14 April 2021

2021-04-14T05:29:57Z

←Older revision		Revision as of 05:29, 14 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.		Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.

OCA at 04:23, 7 April 2021

2021-04-07T04:23:23Z

←Older revision		Revision as of 04:23, 7 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lwc is ON HOLD ~~until Paper Publication~~	+	The entry 6lwc is ON HOLD

	Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.		Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Zhu, C.X]]		[[Category: Zhu, C.X]]
-	[[Category: Yi, C.Q]]
	[[Category: Gao, Y.Q]]		[[Category: Gao, Y.Q]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]
	[[Category: Zhang, X.X]]		[[Category: Zhang, X.X]]
	[[Category: Liu, M.H]]		[[Category: Liu, M.H]]
		+	[[Category: Yi, C.Q]]

OCA at 07:58, 26 February 2020

2020-02-26T07:58:54Z

←Older revision		Revision as of 07:58, 26 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.		Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.

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

2020-02-13T02:36:08Z

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

←Older revision

Revision as of 02:36, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lwc is ON HOLD Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q. Description: Crystal structure of human NEIL1(P2G, E3Q, ...

2020-02-13T02:36:06Z

New page: '''Unreleased structure''' The entry 6lwc is ON HOLD Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q. Description: Crystal structure of human NEIL1(P2G, E3Q, ...

New page

'''Unreleased structure'''

The entry 6lwc is ON HOLD

Authors: Liu, M.H., Zhang, J., Zhu, C.X., Zhang, X.X., Gao, Y.Q., Yi, C.Q.

Description: Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp)
[[Category: Unreleased Structures]]
[[Category: Zhu, C.X]]
[[Category: Yi, C.Q]]
[[Category: Gao, Y.Q]]
[[Category: Zhang, J]]
[[Category: Zhang, X.X]]
[[Category: Liu, M.H]]