5b88 - Revision history

OCA at 06:41, 31 May 2023

OCA — Wed, 31 May 2023 06:41:46 GMT

←Older revision		Revision as of 06:41, 31 May 2023
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	==RRM-like domain of DEAD-box protein, CsdA==		==RRM-like domain of DEAD-box protein, CsdA==
-	<StructureSection load='5b88' size='340' side='right' caption='[[5b88~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5b88' size='340' side='right'caption='[[5b88]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b88]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B88 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B88 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b88]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B88 FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>~~	+	</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=5b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b88 OCA], [https://pdbe.org/5b88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b88 RCSB], [https://www.ebi.ac.uk/pdbsum/5b88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b88 ProSAT]</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=5b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b88 OCA], [~~http~~://pdbe.org/5b88 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b88 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b88 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b88 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI]] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref>	+	[https://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:

	==See Also==		==See Also==
-	*[[Helicase\|Helicase]]	+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~RNA helicase~~]]	+	[[Category: Large Structures]]
-	[[Category: Peng, J]]	+	[[Category: Peng J]]
-	[[Category: Shi, Y]]	+	[[Category: Shi Y]]
-	[[Category: Tang, Y]]	+	[[Category: Tang Y]]
-	[[Category: Wu, J]]	+	[[Category: Wu J]]
-	[[Category: Xu, L]]	+	[[Category: Xu L]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	~~[[Category: Rna binding protein~~]]	+

OCA at 07:03, 12 December 2018

OCA — Wed, 12 Dec 2018 07:03:14 GMT

←Older revision		Revision as of 07:03, 12 December 2018
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI]] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref>		[[http://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI]] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex.
		+
		+	Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.,Xu L, Wang L, Peng J, Li F, Wu L, Zhang B, Lv M, Zhang J, Gong Q, Zhang R, Zuo X, Zhang Z, Wu J, Tang Y, Shi Y Structure. 2017 Dec 5;25(12):1795-1808.e5. doi: 10.1016/j.str.2017.09.013. Epub, 2017 Oct 26. PMID:29107486<ref>PMID:29107486</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5b88" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase\|Helicase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:31, 16 November 2017

OCA — Thu, 16 Nov 2017 11:31:42 GMT

←Older revision		Revision as of 11:31, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5b88 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==RRM-like domain of DEAD-box protein, CsdA==
-		+	<StructureSection load='5b88' size='340' side='right' caption='[[5b88]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5b88]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B88 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">deaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5b88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b88 OCA], [http://pdbe.org/5b88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b88 RCSB], [http://www.ebi.ac.uk/pdbsum/5b88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b88 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEAD_ECOLI DEAD_ECOLI]] DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation. Exhibits RNA-stimulated ATP hydrolysis and RNA unwinding activity at low temperature. Involved in 50S ribosomal subunit assembly, acting after SrmB, and could also play a role in the biogenesis of the 30S ribosomal subunit. In addition, is involved in mRNA decay, via formation of a cold-shock degradosome with RNase E. Also stimulates translation of some mRNAs, probably at the level of initiation.[HAMAP-Rule:MF_00964]<ref>PMID:10216955</ref> <ref>PMID:15148362</ref> <ref>PMID:15196029</ref> <ref>PMID:15554978</ref> <ref>PMID:17259309</ref> <ref>PMID:8552679</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: RNA helicase]]
		+	[[Category: Peng, J]]
		+	[[Category: Shi, Y]]
		+	[[Category: Tang, Y]]
		+	[[Category: Wu, J]]
		+	[[Category: Xu, L]]
		+	[[Category: Zhang, J]]
		+	[[Category: Rna binding protein]]

OCA at 19:33, 12 July 2016

OCA — Tue, 12 Jul 2016 19:33:11 GMT

←Older revision		Revision as of 19:33, 12 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b88 is ON HOLD	+	The entry 5b88 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5b88" [edit=sysop:move=sysop]

OCA — Thu, 23 Jun 2016 16:49:06 GMT

Protected "5b88" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:49, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5b88 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 23 Jun 2016 16:49:05 GMT

New page: '''Unreleased structure''' The entry 5b88 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5b88 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]