5v9x - Revision history

OCA at 14:31, 6 March 2024

OCA — Wed, 06 Mar 2024 14:31:42 GMT

←Older revision		Revision as of 14:31, 6 March 2024
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	==Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP==		==Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP==
-	<StructureSection load='5v9x' size='340' side='right' caption='[[5v9x]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5v9x' size='340' side='right'caption='[[5v9x]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v9x]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_smegmatis"_trevisan_1889 "bacillus~~ smegmatis~~" trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v9x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V9X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.797Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lhr, ERS451418_01790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=5v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9x OCA], [https://pdbe.org/5v9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v9x RCSB], [https://www.ebi.ac.uk/pdbsum/5v9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9x ProSAT]</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=5v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9x OCA], [~~http~~://pdbe.org/5v9x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v9x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v9x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9x ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0QT91_MYCS2 A0QT91_MYCS2]
-	Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes en route. ATPase, translocase and helicase activities are encompassed within the N-terminal 856-amino acid segment. The crystal structure of Lhr-(1-856) in complex with AMPPNP*Mg2+ and ssDNA defines a new helicase family. The enzyme comprises two N-terminal RecA-like modules, a winged helix (WH) domain and a unique C-terminal domain. The 3' ssDNA end binds in a crescent-shaped groove at the interface between the first RecA domain and the WH domain and tracks 5' into a groove between the second RecA and C domains. A kissing interaction between the second RecA and C domains forms an aperture that demarcates a putative junction between the loading strand tail and the duplex, with the first duplex nucleoside bookended by stacking on Trp597. Intercalation of Ile528 between nucleosides of the loading strand creates another bookend. Coupling of ATP hydrolysis to RNA:~~DNA unwinding is dependent on Trp597 and Ile528, and on Thr145 and Arg279 that contact phosphates of the loading strand~~. ~~The structural and functional data suggest a ratchet mechanism of translocation and unwinding coupled to ATP-driven domain movements~~.	+

-	Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases.,Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman S Nucleic Acids Res. 2017 Nov 20. pii: 4641910. doi: 10.1093/nar/gkx1163. PMID:29165676<ref>PMID:29165676</ref>	+	==See Also==
-		+	*[[Helicase 3D structures\|Helicase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5v9x" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ smegmatis ~~trevisan 1889~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: Ferrao, R]]	+	[[Category: Unidentified]]
-	[[Category: Jacewicz, A]]	+	[[Category: Ferrao R]]
-	[[Category: Ordonez, H]]	+	[[Category: Jacewicz A]]
-	[[Category: Shuman, S]]	+	[[Category: Ordonez H]]
-	~~[[Category: Helicase]]~~	+	[[Category: Shuman S]]
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 20:48, 24 January 2018

OCA — Wed, 24 Jan 2018 20:48:52 GMT

←Older revision		Revision as of 20:48, 24 January 2018
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	<StructureSection load='5v9x' size='340' side='right' caption='[[5v9x]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5v9x' size='340' side='right' caption='[[5v9x]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v9x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v9x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lhr, ERS451418_01790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=5v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9x OCA], [http://pdbe.org/5v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9x RCSB], [http://www.ebi.ac.uk/pdbsum/5v9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9x ProSAT]</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=5v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9x OCA], [http://pdbe.org/5v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9x RCSB], [http://www.ebi.ac.uk/pdbsum/5v9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9x ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: RNA helicase]]		[[Category: RNA helicase]]
	[[Category: Ferrao, R]]		[[Category: Ferrao, R]]

OCA at 07:14, 6 December 2017

OCA — Wed, 06 Dec 2017 07:14:58 GMT

←Older revision		Revision as of 07:14, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v9x is ~~ON HOLD until Paper~~ Publication	+	==Structure of Mycobacterium smegmatis helicase Lhr bound to ssDNA and AMP-PNP==
		+	<StructureSection load='5v9x' size='340' side='right' caption='[[5v9x]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v9x]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V9X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </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=5v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v9x OCA], [http://pdbe.org/5v9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v9x RCSB], [http://www.ebi.ac.uk/pdbsum/5v9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v9x ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes en route. ATPase, translocase and helicase activities are encompassed within the N-terminal 856-amino acid segment. The crystal structure of Lhr-(1-856) in complex with AMPPNP*Mg2+ and ssDNA defines a new helicase family. The enzyme comprises two N-terminal RecA-like modules, a winged helix (WH) domain and a unique C-terminal domain. The 3' ssDNA end binds in a crescent-shaped groove at the interface between the first RecA domain and the WH domain and tracks 5' into a groove between the second RecA and C domains. A kissing interaction between the second RecA and C domains forms an aperture that demarcates a putative junction between the loading strand tail and the duplex, with the first duplex nucleoside bookended by stacking on Trp597. Intercalation of Ile528 between nucleosides of the loading strand creates another bookend. Coupling of ATP hydrolysis to RNA:DNA unwinding is dependent on Trp597 and Ile528, and on Thr145 and Arg279 that contact phosphates of the loading strand. The structural and functional data suggest a ratchet mechanism of translocation and unwinding coupled to ATP-driven domain movements.

-	~~Authors~~:	+	Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases.,Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman S Nucleic Acids Res. 2017 Nov 20. pii: 4641910. doi: 10.1093/nar/gkx1163. PMID:29165676<ref>PMID:29165676</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5v9x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA helicase]]
		+	[[Category: Ferrao, R]]
		+	[[Category: Jacewicz, A]]
		+	[[Category: Ordonez, H]]
		+	[[Category: Shuman, S]]
		+	[[Category: Helicase]]
		+	[[Category: Hydrolase-dna complex]]

OCA at 13:57, 27 September 2017

OCA — Wed, 27 Sep 2017 13:57:27 GMT

←Older revision		Revision as of 13:57, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v9x is ON HOLD	+	The entry 5v9x is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v9x" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:50:30 GMT

Protected "5v9x" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:50, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v9x is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 11:50:29 GMT

New page: '''Unreleased structure''' The entry 5v9x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v9x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]