2z41 - Revision history

OCA at 13:56, 13 March 2024

OCA — Wed, 13 Mar 2024 13:56:03 GMT

←Older revision		Revision as of 13:56, 13 March 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3' to 5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 A using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.
-
-	Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.,Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M Protein Sci. 2008 Jan;17(1):136-45. Epub 2007 Nov 27. PMID:18042682<ref>PMID:18042682</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2z41" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:46, 20 September 2023

OCA — Wed, 20 Sep 2023 18:46:00 GMT

←Older revision		Revision as of 18:46, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>		<StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.51Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Kakuta, Y]]	+	[[Category: Kakuta Y]]
-	[[Category: Kimura, M]]	+	[[Category: Kimura M]]
-	[[Category: Nakashima, T]]	+	[[Category: Nakashima T]]
-	[[Category: Tanaka, I]]	+	[[Category: Tanaka I]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Dna helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Rna helicase~~]]	+

OCA at 10:45, 8 December 2021

OCA — Wed, 08 Dec 2021 10:45:18 GMT

←Older revision		Revision as of 10:45, 8 December 2021
Line 1:		Line 1:

	==Crystal Structure Analysis of the Ski2-type RNA helicase==		==Crystal Structure Analysis of the Ski2-type RNA helicase==
-	<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>	+	<StructureSection load='2z41' size='340' side='right'caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [~~http~~://pdbe.org/2z41 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [https://pdbe.org/2z41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [https://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Kakuta, Y]]		[[Category: Kakuta, Y]]

OCA at 07:17, 18 October 2016

OCA — Tue, 18 Oct 2016 07:17:22 GMT

←Older revision		Revision as of 07:17, 18 October 2016
Line 3:		Line 3:
	<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>		<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrho Pyrho~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~PYRHO~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [http://pdbe.org/2z41 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [http://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [http://pdbe.org/2z41 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [http://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrho~~]]	+	[[Category: Pyrococcus horikoshii]]
	[[Category: Kakuta, Y]]		[[Category: Kakuta, Y]]
	[[Category: Kimura, M]]		[[Category: Kimura, M]]

OCA at 16:03, 11 August 2016

OCA — Thu, 11 Aug 2016 16:03:18 GMT

←Older revision		Revision as of 16:03, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure Analysis of the Ski2-type RNA helicase==		==Crystal Structure Analysis of the Ski2-type RNA helicase==
	<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>		<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~Pyrococcus horikoshii OT3~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [http://www.ebi.ac.uk/pdbsum/2z41 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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [http://pdbe.org/2z41 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [http://www.ebi.ac.uk/pdbsum/2z41 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z41 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 2z41" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus horikoshii ot3~~]]	+	[[Category: Pyrho]]
	[[Category: Kakuta, Y]]		[[Category: Kakuta, Y]]
	[[Category: Kimura, M]]		[[Category: Kimura, M]]

OCA at 10:17, 25 January 2015

OCA — Sun, 25 Jan 2015 10:17:49 GMT

←Older revision		Revision as of 10:17, 25 January 2015
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii ot3]]		[[Category: Pyrococcus horikoshii ot3]]
-	[[Category: Kakuta, Y.]]	+	[[Category: Kakuta, Y]]
-	[[Category: Kimura, M.]]	+	[[Category: Kimura, M]]
-	[[Category: Nakashima, T.]]	+	[[Category: Nakashima, T]]
-	[[Category: Tanaka, I.]]	+	[[Category: Tanaka, I]]
-	[[Category: Yao, M.]]	+	[[Category: Yao, M]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Dna helicase]]		[[Category: Dna helicase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Rna helicase]]		[[Category: Rna helicase]]

OCA at 11:56, 29 October 2014

OCA — Wed, 29 Oct 2014 11:56:55 GMT

←Older revision		Revision as of 11:56, 29 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2z41.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure Analysis of the Ski2-type RNA helicase==
		+	<StructureSection load='2z41' size='340' side='right' caption='[[2z41]], [[Resolution\|resolution]] 3.51Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z41 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii OT3])</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=2z41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z41 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z41 RCSB], [http://www.ebi.ac.uk/pdbsum/2z41 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Ski complex composed of Ski2p, Ski3p, and Ski8p plays an essential role in the 3' to 5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in the DExD/H-box protein families and conserved in eukarya as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it to apparent homogeneity. Ph1280p exhibits DNA/RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C. The crystal structure of Ph1280p has been solved at a resolution of 3.5 A using single-wavelength anomalous dispersion (SAD) and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs, while the two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2-like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.

-	~~{{STRUCTURE_2z41\| PDB=2z41 \| SCENE= }}~~	+	Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.,Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M Protein Sci. 2008 Jan;17(1):136-45. Epub 2007 Nov 27. PMID:18042682<ref>PMID:18042682</ref>

-	~~===Crystal Structure Analysis~~ of the ~~Ski2-type RNA helicase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18042682}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[2z41]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA].~~	+	</StructureSection>
	[[Category: Pyrococcus horikoshii ot3]]		[[Category: Pyrococcus horikoshii ot3]]
	[[Category: Kakuta, Y.]]		[[Category: Kakuta, Y.]]

OCA: Protected "2z41" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:20:10 GMT

Protected "2z41" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:20, 7 January 2013

OCA at 19:20, 7 January 2013

OCA — Mon, 07 Jan 2013 19:20:08 GMT

←Older revision		Revision as of 19:20, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z41.png\|left\|200px]]		[[Image:2z41.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z41", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2z41\| PDB=2z41 \| SCENE= }}		{{STRUCTURE_2z41\| PDB=2z41 \| SCENE= }}

	===Crystal Structure Analysis of the Ski2-type RNA helicase===		===Crystal Structure Analysis of the Ski2-type RNA helicase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18042682}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18042682 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18042682}}		{{ABSTRACT_PUBMED_18042682}}

	==About this Structure==		==About this Structure==
-	~~2Z41 is a~~ [[~~Single protein~~]] structure of sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA].	+	[[2z41]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z41 OCA].
-		+	[[Category: Pyrococcus horikoshii ot3]]
-	~~==Reference==~~	+
-	Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3., Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M, Protein Sci. 2008 Jan;17(1):136-45. Epub 2007 Nov 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18042682 18042682]	+
-	[[Category: Pyrococcus horikoshii]]	+
-	~~[[Category: Single protein~~]]	+
	[[Category: Kakuta, Y.]]		[[Category: Kakuta, Y.]]
	[[Category: Kimura, M.]]		[[Category: Kimura, M.]]
Line 35:		Line 19:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Rna helicase]]		[[Category: Rna helicase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:08:43 2008''

OCA at 06:08, 28 July 2008

OCA — Mon, 28 Jul 2008 06:08:47 GMT

←Older revision		Revision as of 06:08, 28 July 2008
Line 1:		Line 1:
-	[[Image:2z41.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2z41.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2z41\| PDB=2z41 \| SCENE= }}		{{STRUCTURE_2z41\| PDB=2z41 \| SCENE= }}

-	~~'''~~Crystal Structure Analysis of the Ski2-type RNA helicase~~'''~~	+	===Crystal Structure Analysis of the Ski2-type RNA helicase===


-	~~==Overview==~~	+	<!--
-	The ~~Ski complex composed of Ski2p~~, ~~Ski3p~~, ~~and Ski8p plays an essential role in~~ the 3' to ~~5' cytoplasmic mRNA degradation pathway in yeast. Ski2p is a putative RNA helicase, belonging in~~ the ~~DExD/H-box protein families and conserved in eukarya~~ as well as in archaea. The gene product (Ph1280p) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 shows sequence homology with Ski2p, sharing 22.6% identical amino acids with a central region of Ski2p. In order to gain structural information about the Ski2p-like RNA helicase, we overproduced Ph1280p in Escherichia coli cells, and purified it ~~to apparent homogeneity. Ph1280p exhibits DNA~~/~~RNA-dependent ATPase activity with an optimal temperature at approximately 90 degrees C~~. ~~The crystal structure of Ph1280p has been solved at a resolution of 3~~.~~5 A using single-wavelength anomalous dispersion (SAD~~) ~~and selenomethionyl (Se-Met)-substituted protein. Ph1280p comprises four subdomains; the two N-terminal subdomains (N1 and N2) fold into an RecA-like architecture with the conserved helicase motifs~~, ~~while~~ the ~~two C-terminal subdomains (C1 and C2) fold into alpha-helical structures containing a winged helix (WH)-fold and helix-hairpin-helix (HhH)-fold, respectively~~. Although the structure of each of the Ph1280p subdomains can be individually superimposed on the corresponding domains in other helicases, such as the Escherichia coli DNA helicase RecQ, the relative orientation of the helicase and C-~~terminal subdomains in Ph1280p is significantly different from that of other helicases. This structural feature is implicated in substrate specificity for the Ski2~~-~~like helicase and would play a critical role in the 3' to 5' cytoplasmic mRNA degradation in the Ski complex.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18042682}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18042682 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18042682}}

	==About this Structure==		==About this Structure==
Line 31:		Line 35:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Rna helicase]]		[[Category: Rna helicase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:08:43 2008''