5yu2 - Revision history

OCA at 08:37, 22 November 2023

OCA — Wed, 22 Nov 2023 08:37:44 GMT

←Older revision		Revision as of 08:37, 22 November 2023
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	==Structure of Ribonuclease YabJ==		==Structure of Ribonuclease YabJ==
-	<StructureSection load='5yu2' size='340' side='right' caption='[[5yu2]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5yu2' size='340' side='right'caption='[[5yu2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yu2]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staam Staam~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YU2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yu2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YU2 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SAV0497 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=158878 STAAM])~~</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]] 1.75Å</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=5yu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yu2 OCA], [~~http~~://pdbe.org/5yu2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yu2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yu2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yu2 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=5yu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yu2 OCA], [https://pdbe.org/5yu2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yu2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yu2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yu2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H3JTJ5_STAAM A0A0H3JTJ5_STAAM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staam~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kim, H J~~]]	+	[[Category: Staphylococcus aureus subsp. aureus Mu50]]
-	[[Category: ~~Kwon, A R~~]]	+	[[Category: Kim HJ]]
-	[[Category: ~~Lee, B J~~]]	+	[[Category: Kwon AR]]
-	[[Category: ~~Gene regulation]]~~	+	[[Category: Lee BJ]]
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Sav0497]]~~	+
-	~~[[Category: Yabj~~]]	+

OCA at 07:08, 31 October 2018

OCA — Wed, 31 Oct 2018 07:08:18 GMT

←Older revision		Revision as of 07:08, 31 October 2018
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	<StructureSection load='5yu2' size='340' side='right' caption='[[5yu2]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5yu2' size='340' side='right' caption='[[5yu2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yu2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yu2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Staam Staam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YU2 FirstGlance]. <br>
-	</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=5yu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yu2 OCA], [http://pdbe.org/5yu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yu2 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAV0497 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=5yu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yu2 OCA], [http://pdbe.org/5yu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yu2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Staam]]
	[[Category: Kim, H J]]		[[Category: Kim, H J]]
	[[Category: Kwon, A R]]		[[Category: Kwon, A R]]

OCA at 07:54, 26 September 2018

OCA — Wed, 26 Sep 2018 07:54:53 GMT

←Older revision		Revision as of 07:54, 26 September 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yu2 is ~~ON HOLD until Paper~~ Publication	+	==Structure of Ribonuclease YabJ==
		+	<StructureSection load='5yu2' size='340' side='right' caption='[[5yu2]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yu2]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YU2 FirstGlance]. <br>
		+	</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=5yu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yu2 OCA], [http://pdbe.org/5yu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yu2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The characteristic fold of a protein is the decisive factor for its biological function. However, small structural changes to amino acids can also affect their function, for example in the case of post- translational modification (PTM). Many different types of PTMs are known, but for some, including chlorination, studies elucidating their importance are limited. A recent study revealed that the YjgF family member RidA from Escherichia coli shows chaperone activity after chlorination. Thus, to identify the functional and structural difference of RidA upon chlorination, we studied a RidA homologue from Staphylococcus aureus : YabJ. The overall structure of S. aureus YabJ was similar to other members of the YjgF family, showing deep pockets on its surface, and the residues composing the pockets were well conserved. S. aureus YabJ was highly stable after chlorination and the chlorinated state is reversible by treatment with DTT. However, it shows no chaperone activity after chlorination. Instead, YabJ from S. aureus shows chlorination-induced ribonuclease activity, and the activity is diminished after subsequent reduction. Even though the yabJ genes from Staphylococcus and Bacillus are clustered with regulators that are expected to code nucleic acid-interacting proteins, the nucleic acid-related activity of bacterial RidA has not been identified before. From our study, we revealed the structure and function of S. aureus YabJ as a novel chlorination-activated ribonuclease. This study will contribute to an in-depth understanding of chlorination as a post-translational modification.

-	~~Authors: Kim, H.J~~., Kwon, A.R.~~, Lee, B~~.J.	+	A novel chlorination-induced ribonuclease YabJ from Staphylococcus aureus.,Kim HJ, Kwon AR, Lee BJ Biosci Rep. 2018 Sep 10. pii: BSR20180768. doi: 10.1042/BSR20180768. PMID:30201692<ref>PMID:30201692</ref>

-	~~Description: Structure~~ of ~~Ribonuclease YabJ~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Lee, B.J]]	+	<div class="pdbe-citations 5yu2" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kwon, A.R~~]]	+	== References ==
-	[[Category: ~~Kim, H.J~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, H J]]
		+	[[Category: Kwon, A R]]
		+	[[Category: Lee, B J]]
		+	[[Category: Gene regulation]]
		+	[[Category: Ribonuclease]]
		+	[[Category: Sav0497]]
		+	[[Category: Yabj]]

OCA at 05:46, 13 December 2017

OCA — Wed, 13 Dec 2017 05:46:44 GMT

←Older revision		Revision as of 05:46, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yu2 is ON HOLD	+	The entry 5yu2 is ON HOLD until Paper Publication

	Authors: Kim, H.J., Kwon, A.R., Lee, B.J.		Authors: Kim, H.J., Kwon, A.R., Lee, B.J.

-	Description: YabJ	+	Description: Structure of Ribonuclease YabJ
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Lee, B.J]]		[[Category: Lee, B.J]]
	[[Category: Kwon, A.R]]		[[Category: Kwon, A.R]]
	[[Category: Kim, H.J]]		[[Category: Kim, H.J]]

OCA: Protected "5yu2" [edit=sysop:move=sysop]

OCA — Wed, 29 Nov 2017 04:58:40 GMT

Protected "5yu2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:58, 29 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yu2 is ON HOLD Authors: Kim, H.J., Kwon, A.R., Lee, B.J. Description: YabJ Category: Unreleased Structures Category: Lee, B.J [[Category: ...

OCA — Wed, 29 Nov 2017 04:58:39 GMT

New page: '''Unreleased structure''' The entry 5yu2 is ON HOLD Authors: Kim, H.J., Kwon, A.R., Lee, B.J. Description: YabJ Category: Unreleased Structures Category: Lee, B.J [[Category: ...

New page

'''Unreleased structure'''

The entry 5yu2 is ON HOLD

Authors: Kim, H.J., Kwon, A.R., Lee, B.J.

Description: YabJ
[[Category: Unreleased Structures]]
[[Category: Lee, B.J]]
[[Category: Kwon, A.R]]
[[Category: Kim, H.J]]