6dgb - Revision history

OCA at 14:34, 13 March 2024

2024-03-13T14:34:07Z

←Older revision		Revision as of 14:34, 13 March 2024
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	<StructureSection load='6dgb' size='340' side='right'caption='[[6dgb]], [[Resolution\|resolution]] 2.52Å' scene=''>		<StructureSection load='6dgb' size='340' side='right'caption='[[6dgb]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dgb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dgb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DGB FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>IS1535 TnpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884~~])</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]] 2.52Å</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=6dgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgb OCA], [~~http~~://pdbe.org/6dgb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dgb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dgb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgb 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=6dgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgb OCA], [https://pdbe.org/6dgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dgb RCSB], [https://www.ebi.ac.uk/pdbsum/6dgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgb ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/I6WZS4_MYCTU I6WZS4_MYCTU]
-	IS607-family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal alpha-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.	+
-		+
-	Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition.,Chen W, Mandali S, Hancock SP, Kumar P, Collazo M, Cascio D, Johnson RC Elife. 2018 Oct 5;7. pii: ~~39611. doi: 10.7554~~/~~eLife.39611. PMID:30289389<ref>PMID:30289389<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6dgb" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cascio, D~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Chen, W Y~~]]	+	[[Category: Cascio D]]
-	[[Category: ~~Hancock, S P~~]]	+	[[Category: Chen WY]]
-	[[Category: ~~Johnson, R C~~]]	+	[[Category: Hancock SP]]
-	[[Category: ~~607-like serine recombinase]]~~	+	[[Category: Johnson RC]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:10, 3 April 2019

2019-04-03T08:10:51Z

←Older revision		Revision as of 08:10, 3 April 2019
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	==Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase==		==Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase==
-	<StructureSection load='6dgb' size='340' side='right' caption='[[6dgb]], [[Resolution\|resolution]] 2.52Å' scene=''>	+	<StructureSection load='6dgb' size='340' side='right'caption='[[6dgb]], [[Resolution\|resolution]] 2.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dgb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGB 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=6dgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgb OCA], [http://pdbe.org/6dgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgb RCSB], [http://www.ebi.ac.uk/pdbsum/6dgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgb ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IS1535 TnpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6dgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgb OCA], [http://pdbe.org/6dgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgb RCSB], [http://www.ebi.ac.uk/pdbsum/6dgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	IS607-family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal alpha-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.
		+
		+	Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition.,Chen W, Mandali S, Hancock SP, Kumar P, Collazo M, Cascio D, Johnson RC Elife. 2018 Oct 5;7. pii: 39611. doi: 10.7554/eLife.39611. PMID:30289389<ref>PMID:30289389</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dgb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]
	[[Category: Chen, W Y]]		[[Category: Chen, W Y]]

OCA at 07:38, 18 July 2018

2018-07-18T07:38:54Z

←Older revision		Revision as of 07:38, 18 July 2018
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-	'''Unreleased structure'''

-	~~The entry 6dgb is ON HOLD until Paper Publication~~	+	==Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase==
-		+	<StructureSection load='6dgb' size='340' side='right' caption='[[6dgb]], [[Resolution\|resolution]] 2.52Å' scene=''>
-	~~Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DGB FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase	+	</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=6dgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dgb OCA], [http://pdbe.org/6dgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dgb RCSB], [http://www.ebi.ac.uk/pdbsum/6dgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dgb ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Hancock, S~~.P]]	+	__TOC__
-	[[~~Category~~: ~~Chen~~, W.Y]]	+	</StructureSection>
	[[Category: Cascio, D]]		[[Category: Cascio, D]]
-	[[Category: Johnson, R.C]]	+	[[Category: Chen, W Y]]
		+	[[Category: Hancock, S P]]
		+	[[Category: Johnson, R C]]
		+	[[Category: 607-like serine recombinase]]
		+	[[Category: Hydrolase]]

OCA at 05:35, 14 June 2018

2018-06-14T05:35:47Z

←Older revision		Revision as of 05:35, 14 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C.		Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C.
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	[[Category: Hancock, S.P]]		[[Category: Hancock, S.P]]
	[[Category: Chen, W.Y]]		[[Category: Chen, W.Y]]
-	[[Category: Johnson, R.C]]
	[[Category: Cascio, D]]		[[Category: Cascio, D]]
		+	[[Category: Johnson, R.C]]

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

2018-05-23T06:05:09Z

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

←Older revision

Revision as of 06:05, 23 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dgb is ON HOLD Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C. Description: Crystal structure of the C-terminal catalytic domain of ...

2018-05-23T06:05:07Z

New page: '''Unreleased structure''' The entry 6dgb is ON HOLD Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C. Description: Crystal structure of the C-terminal catalytic domain of ...

New page

'''Unreleased structure'''

The entry 6dgb is ON HOLD

Authors: Chen, W.Y., Hancock, S.P., Cascio, D., Johnson, R.C.

Description: Crystal structure of the C-terminal catalytic domain of IS1535 TnpA, an IS607-like serine recombinase
[[Category: Unreleased Structures]]
[[Category: Hancock, S.P]]
[[Category: Chen, W.Y]]
[[Category: Johnson, R.C]]
[[Category: Cascio, D]]