3wdg - Revision history

OCA at 18:20, 18 October 2023

OCA — Wed, 18 Oct 2023 18:20:44 GMT

←Older revision		Revision as of 18:20, 18 October 2023
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	==Staphylococcus aureus UDG / UGI complex==		==Staphylococcus aureus UDG / UGI complex==
-	<StructureSection load='3wdg' size='340' side='right' caption='[[3wdg]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3wdg' size='340' side='right'caption='[[3wdg]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wdg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~] and [~~http~~://en.wikipedia.org/wiki/~~Staar Staar~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WDG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wdg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] and [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_MRSA252 Staphylococcus aureus subsp. aureus MRSA252]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WDG FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3wdf\|3wdf]]</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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ung, SAR0586 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282458 STAAR])</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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [https://pdbe.org/3wdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [https://www.ebi.ac.uk/pdbsum/3wdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdg 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/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2~~.27 3.2.2.27] </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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [~~http~~://pdbe.org/3wdg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wdg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdg ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UNG_STAAR UNG_STAAR]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).	+	[https://www.uniprot.org/uniprot/UNG_STAAR UNG_STAAR] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]	+
-	*[[Uracil-DNA glycosylase inhibitor\|Uracil-DNA glycosylase inhibitor]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staar~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Uracil-DNA glycosylase~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Ko, T P~~]]	+	[[Category: Staphylococcus aureus subsp. aureus MRSA252]]
-	[[Category: ~~Wang, A H.J~~]]	+	[[Category: Ko TP]]
-	[[Category: Wang~~, H C~~]]	+	[[Category: Wang AHJ]]
-	[[Category: ~~Hydrolase-hydrolase inhibitor complex]]~~	+	[[Category: Wang HC]]
-	~~[[Category: Uracil-dna glycosylase]]~~	+
-	~~[[Category: Uracil-dna glycosylase inhibitor~~]]	+

OCA at 17:02, 5 August 2016

OCA — Fri, 05 Aug 2016 17:02:45 GMT

←Older revision		Revision as of 17:02, 5 August 2016
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		+
	==Staphylococcus aureus UDG / UGI complex==		==Staphylococcus aureus UDG / UGI complex==
	<StructureSection load='3wdg' size='340' side='right' caption='[[3wdg]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3wdg' size='340' side='right' caption='[[3wdg]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ung, SAR0586 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282458 STAAR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ung, SAR0586 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282458 STAAR])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [http://www.ebi.ac.uk/pdbsum/3wdg 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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [http://pdbe.org/3wdg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [http://www.ebi.ac.uk/pdbsum/3wdg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 3wdg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[DNA glycosylase\|DNA glycosylase]]
	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]		*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
	*[[Uracil-DNA glycosylase inhibitor\|Uracil-DNA glycosylase inhibitor]]		*[[Uracil-DNA glycosylase inhibitor\|Uracil-DNA glycosylase inhibitor]]

OCA at 20:30, 25 December 2014

OCA — Thu, 25 Dec 2014 20:30:16 GMT

←Older revision		Revision as of 20:30, 25 December 2014
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	<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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [http://www.ebi.ac.uk/pdbsum/3wdg 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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [http://www.ebi.ac.uk/pdbsum/3wdg PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UNG_STAAR UNG_STAAR]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:52, 21 December 2014

OCA — Sun, 21 Dec 2014 17:52:13 GMT

←Older revision		Revision as of 17:52, 21 December 2014
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-	~~{{STRUCTURE_3wdg\| PDB~~=3wdg \| ~~SCENE~~= }}	+	==Staphylococcus aureus UDG / UGI complex==
-	===~~Staphylococcus~~ aureus ~~UDG~~ / ~~UGI complex~~===	+	<StructureSection load='3wdg' size='340' side='right' caption='[[3wdg]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24150946}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wdg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885] and [http://en.wikipedia.org/wiki/Staar Staar]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WDG FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wdf\|3wdf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ung, SAR0586 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282458 STAAR])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=3wdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wdg RCSB], [http://www.ebi.ac.uk/pdbsum/3wdg PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA mimic proteins are unique factors that control the DNA binding activity of target proteins by directly occupying their DNA binding sites. The extremely divergent amino acid sequences of the DNA mimics make these proteins hard to predict, and although they are likely to be ubiquitous, to date, only a few have been reported and functionally analyzed. Here we used a bioinformatic approach to look for potential DNA mimic proteins among previously reported protein structures. From approximately 14 candidates, we selected the Staphylococcus conserved hypothetical protein SSP0047, and used proteomic and structural approaches to show that it is a novel DNA mimic protein. In Staphylococcus aureus, we found that this protein acts as a uracil-DNA glycosylase inhibitor, and therefore named it S. aureus uracil-DNA glycosylase inhibitor (SAUGI). We also determined and analyzed the complex structure of SAUGI and S. aureus uracil-DNA glycosylase (SAUDG). Subsequent BIAcore studies further showed that SAUGI has a high binding affinity to both S. aureus and human UDG. The two uracil-DNA glycosylase inhibitors (UGI and p56) previously known to science were both found in Bacillus phages, and this is the first report of a bacterial DNA mimic that may regulate SAUDG's functional roles in DNA repair and host defense.

-	~~==Function==~~	+	Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor.,Wang HC, Hsu KC, Yang JM, Wu ML, Ko TP, Lin SR, Wang AH Nucleic Acids Res. 2014 Jan 1;42(2):1354-64. doi: 10.1093/nar/gkt964. Epub 2013, Oct 22. PMID:24150946<ref>PMID:24150946</ref>
-	~~[[http://www.uniprot.org/uniprot/UNG_STAAR UNG_STAAR]] Excises uracil residues from the DNA which can arise~~ as a ~~result of misincorporation of dUMP residues by~~ DNA ~~polymerase or due to deamination of cytosine~~ (~~By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3wdg]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3WDG OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024150946</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Uracil-DNA glycosylase\|Uracil-DNA glycosylase]]
		+	*[[Uracil-DNA glycosylase inhibitor\|Uracil-DNA glycosylase inhibitor]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Staar]]
	[[Category: Uracil-DNA glycosylase]]		[[Category: Uracil-DNA glycosylase]]
-	[[Category: Ko, T P.]]	+	[[Category: Ko, T P]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Wang, A H.J]]
-	[[Category: Wang, H C.]]	+	[[Category: Wang, H C]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Uracil-dna glycosylase]]		[[Category: Uracil-dna glycosylase]]
	[[Category: Uracil-dna glycosylase inhibitor]]		[[Category: Uracil-dna glycosylase inhibitor]]

OCA at 11:09, 5 February 2014

OCA — Wed, 05 Feb 2014 11:09:08 GMT

←Older revision		Revision as of 11:09, 5 February 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3wdg\| PDB=3wdg \| SCENE= }}
		+	===Staphylococcus aureus UDG / UGI complex===
		+	{{ABSTRACT_PUBMED_24150946}}

-	~~The entry 3wdg is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/UNG_STAAR UNG_STAAR]] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine (By similarity).

-	~~Authors~~: ~~Wang, H.C., Ko, T.P~~.~~, Wang, A~~.H.J.	+	==About this Structure==
		+	[[3wdg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDG OCA].

-	~~Description~~: ~~Staphylococcus aureus UDG~~ / ~~UGI~~ complex	+	==Reference==
		+	<ref group="xtra">PMID:024150946</ref><references group="xtra"/><references/>
		+	[[Category: Uracil-DNA glycosylase]]
		+	[[Category: Ko, T P.]]
		+	[[Category: Wang, A H.J.]]
		+	[[Category: Wang, H C.]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Uracil-dna glycosylase]]
		+	[[Category: Uracil-dna glycosylase inhibitor]]

OCA at 04:39, 18 July 2013

OCA — Thu, 18 Jul 2013 04:39:55 GMT

←Older revision		Revision as of 04:39, 18 July 2013
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wdg is ON HOLD	+	The entry 3wdg is ON HOLD until Paper Publication

	Authors: Wang, H.C., Ko, T.P., Wang, A.H.J.		Authors: Wang, H.C., Ko, T.P., Wang, A.H.J.

	Description: Staphylococcus aureus UDG / UGI complex		Description: Staphylococcus aureus UDG / UGI complex

OCA at 14:41, 10 July 2013

OCA — Wed, 10 Jul 2013 14:41:03 GMT

←Older revision		Revision as of 14:41, 10 July 2013
Line 3:		Line 3:
	The entry 3wdg is ON HOLD		The entry 3wdg is ON HOLD

-	Authors: Wang, H. C. , Ko, T. P. , Wang, A. H. J.	+	Authors: Wang, H.C., Ko, T.P., Wang, A.H.J.

	Description: Staphylococcus aureus UDG / UGI complex		Description: Staphylococcus aureus UDG / UGI complex

OCA: Protected "3wdg" [edit=sysop:move=sysop]

OCA — Sun, 30 Jun 2013 08:23:46 GMT

Protected "3wdg" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:23, 30 June 2013

OCA: New page: '''Unreleased structure''' The entry 3wdg is ON HOLD Authors: Wang, H. C. , Ko, T. P. , Wang, A. H. J. Description: Staphylococcus aureus UDG / UGI complex

OCA — Sun, 30 Jun 2013 08:23:45 GMT

New page: '''Unreleased structure''' The entry 3wdg is ON HOLD Authors: Wang, H. C. , Ko, T. P. , Wang, A. H. J. Description: Staphylococcus aureus UDG / UGI complex

New page

'''Unreleased structure'''

The entry 3wdg is ON HOLD

Authors: Wang, H. C. , Ko, T. P. , Wang, A. H. J.

Description: Staphylococcus aureus UDG / UGI complex