6m4j - Revision history

OCA at 15:15, 29 November 2023

OCA — Wed, 29 Nov 2023 15:15:02 GMT

←Older revision		Revision as of 15:15, 29 November 2023
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	<StructureSection load='6m4j' size='340' side='right'caption='[[6m4j]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6m4j' size='340' side='right'caption='[[6m4j]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m4j]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_700982 Atcc 700982~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m4j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cyclitrophicus Vibrio cyclitrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M4J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6m4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4j OCA], [~~http~~://pdbe.org/6m4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4j ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=6m4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4j OCA], [https://pdbe.org/6m4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m4j RCSB], [https://www.ebi.ac.uk/pdbsum/6m4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6m4j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m4j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cysteine desulfurase 3D structures\|Cysteine desulfurase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 700982]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gao, H~~]]	+	[[Category: Vibrio cyclitrophicus]]
-	[[Category: ~~Liu, L~~]]	+	[[Category: Gao H]]
-	[[Category: ~~Cysteine desulfhydrase]]~~	+	[[Category: Liu L]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 05:46, 13 May 2020

OCA — Wed, 13 May 2020 05:46:31 GMT

←Older revision		Revision as of 05:46, 13 May 2020
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	==SspA in complex with cysteine==		==SspA in complex with cysteine==
-	<StructureSection load='6m4j' size='340' side='right'caption='[[6m4j]]' scene=''>	+	<StructureSection load='6m4j' size='340' side='right'caption='[[6m4j]], [[Resolution\|resolution]] 1.80Å' 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=6M4J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m4j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700982 Atcc 700982]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4J FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6m4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4j OCA], [http://pdbe.org/6m4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4j RCSB], [http://www.ebi.ac.uk/pdbsum/6m4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6m4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4j OCA], [http://pdbe.org/6m4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4j RCSB], [http://www.ebi.ac.uk/pdbsum/6m4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4j ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 A. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 A, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification.IMPORTANCE Apart from its roles in Fe-S cluster assembly, tRNA thiolation, and sulfur-containing cofactor biosynthesis, cysteine desulfurase serves as a sulfur donor in the DNA PT modification, in which a sulfur atom substitutes a nonbridging oxygen in the DNA phosphodiester backbone. The initial sulfur mobilization from l-cysteine is catalyzed by the SspA cysteine desulfurase in the SspABCD-mediated DNA PT modification system. By determining the crystal structure of SspA, the study presents the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor. To overcome the long distance (8.9 A) between the catalytic Cys314 and the cysteine substrate, a conformational change occurs to bring Cys314 to the vicinity of the substrate, allowing for nucleophilic attack.
		+
		+	Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System.,Liu L, Jiang S, Xing M, Chen C, Lai C, Li N, Liu G, Wu D, Gao H, Hong L, Tan P, Chen S, Deng Z, Wu G, Wang L mBio. 2020 Apr 28;11(2). pii: mBio.00488-20. doi: 10.1128/mBio.00488-20. PMID:32345643<ref>PMID:32345643</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m4j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 700982]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gao H]]	+	[[Category: Gao, H]]
-	[[Category: Liu L]]	+	[[Category: Liu, L]]
		+	[[Category: Cysteine desulfhydrase]]
		+	[[Category: Oxidoreductase]]

OCA at 05:40, 22 April 2020

OCA — Wed, 22 Apr 2020 05:40:54 GMT

←Older revision		Revision as of 05:40, 22 April 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6m4j ~~is ON HOLD until Paper Publication~~	+	==SspA in complex with cysteine==
-		+	<StructureSection load='6m4j' size='340' side='right'caption='[[6m4j]]' scene=''>
-	~~Authors~~: ~~Qiong~~, L.L., ~~Yang~~, H.G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M4J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M4J FirstGlance]. <br>
-	~~Description: SspA in complex with cysteine~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6m4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m4j OCA], [http://pdbe.org/6m4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m4j RCSB], [http://www.ebi.ac.uk/pdbsum/6m4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m4j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Yang,~~ H.G]]	+	__TOC__
-	[[Category: ~~Qiong, L.~~L]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gao H]]
		+	[[Category: Liu L]]

OCA at 07:20, 1 April 2020

OCA — Wed, 01 Apr 2020 07:20:50 GMT

←Older revision		Revision as of 07:20, 1 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m4j is ON HOLD	+	The entry 6m4j is ON HOLD until Paper Publication

	Authors: Qiong, L.L., Yang, H.G.		Authors: Qiong, L.L., Yang, H.G.

OCA: Protected "6m4j" [edit=sysop:move=sysop]

OCA — Wed, 18 Mar 2020 08:17:45 GMT

Protected "6m4j" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:17, 18 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m4j is ON HOLD Authors: Qiong, L.L., Yang, H.G. Description: SspA in complex with cysteine Category: Unreleased Structures [[Category: Yang, H...

OCA — Wed, 18 Mar 2020 08:17:44 GMT

New page: '''Unreleased structure''' The entry 6m4j is ON HOLD Authors: Qiong, L.L., Yang, H.G. Description: SspA in complex with cysteine Category: Unreleased Structures [[Category: Yang, H...

New page

'''Unreleased structure'''

The entry 6m4j is ON HOLD

Authors: Qiong, L.L., Yang, H.G.

Description: SspA in complex with cysteine
[[Category: Unreleased Structures]]
[[Category: Yang, H.G]]
[[Category: Qiong, L.L]]