7bbb - Revision history

OCA at 06:11, 19 June 2024

2024-06-19T06:11:59Z

← Older revision		Revision as of 06:11, 19 June 2024
Line 3:		Line 3:
	<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]]' scene=''>		<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7bbb]] 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=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>		<table><tr><td colspan='2'>Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>
	</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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/DBPA_ECOLI DBPA_ECOLI] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]<ref>PMID:11350034</ref> <ref>PMID:11574482</ref> <ref>PMID:15910005</ref> <ref>PMID:18237742</ref> <ref>PMID:19734347</ref> <ref>PMID:20160110</ref> <ref>PMID:8253085</ref> <ref>PMID:9016593</ref> <ref>PMID:9836593</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The adenosine triphosphate (ATP)-dependent DEAD-box RNA helicase DbpA from Escherichia coli functions in ribosome biogenesis. DbpA is targeted to the nascent 50S subunit by an ancillary, carboxyl-terminal RNA recognition motif (RRM) that specifically binds to hairpin 92 (HP92) of the 23S ribosomal RNA (rRNA). The interaction between HP92 and the RRM is required for the helicase activity of the RecA-like core domains of DbpA. Here, we elucidate the structural basis by which DbpA activity is endorsed when the enzyme interacts with the maturing ribosome. We used nuclear magnetic resonance (NMR) spectroscopy to show that the RRM and the carboxyl-terminal RecA-like domain tightly interact. This orients HP92 such that this RNA hairpin can form electrostatic interactions with a positively charged patch in the N-terminal RecA-like domain. Consequently, the enzyme can stably adopt the catalytically important, closed conformation. The substrate binding mode in this complex reveals that a region 5' to helix 90 in the maturing ribosome is specifically targeted by DbpA. Finally, our results indicate that the ribosome maturation defects induced by a dominant negative DbpA mutation are caused by a delayed dissociation of DbpA from the nascent ribosome. Taken together, our findings provide unique insights into the important regulatory mechanism that modulates the activity of DbpA.

	Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome.,Wurm JP, Glowacz KA, Sprangers R Proc Natl Acad Sci U S A. 2021 Aug 31;118(35). pii: 2105961118. doi:, 10.1073/pnas.2105961118. PMID:34453003<ref>PMID:34453003</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7bbb" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Helicase 3D structures\|Helicase 3D structures]]		*[[Helicase 3D structures\|Helicase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Escherichia coli K-12]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sprangers R]]		[[Category: Sprangers R]]
	[[Category: Wurm JP]]		[[Category: Wurm JP]]

OCA at 11:11, 14 June 2023

2023-06-14T11:11:02Z

← Older revision		Revision as of 11:11, 14 June 2023
Line 1:		Line 1:

	==Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA==		==Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA==
	<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>		<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7bbb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7bbb]] 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=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbpA, b1343, JW1337 ([https://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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DBPA_ECOLI DBPA_ECOLI]] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]<ref>PMID:11350034</ref> <ref>PMID:11574482</ref> <ref>PMID:15910005</ref> <ref>PMID:18237742</ref> <ref>PMID:19734347</ref> <ref>PMID:20160110</ref> <ref>PMID:8253085</ref> <ref>PMID:9016593</ref> <ref>PMID:9836593</ref>		[https://www.uniprot.org/uniprot/DBPA_ECOLI DBPA_ECOLI] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]<ref>PMID:11350034</ref> <ref>PMID:11574482</ref> <ref>PMID:15910005</ref> <ref>PMID:18237742</ref> <ref>PMID:19734347</ref> <ref>PMID:20160110</ref> <ref>PMID:8253085</ref> <ref>PMID:9016593</ref> <ref>PMID:9836593</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: RNA helicase]]~~		[[Category: Sprangers R]]
	[[Category: Sprangers, R]]		[[Category: Wurm JP]]
	[[Category: Wurm~~, J P]]~~
	~~[[Category: Dead box helicase]]~~
	~~[[Category: Ribosome biogenesis]]~~
	~~[[Category: Rna]]~~
	~~[[Category: Rna binding protein~~]]

OCA at 06:58, 22 September 2021

2021-09-22T06:58:42Z

← Older revision		Revision as of 06:58, 22 September 2021
Line 1:		Line 1:

	==Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA==		==Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA==
	<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]]' scene=''>		<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' 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=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7bbb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>
	</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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dbpA, b1343, JW1337 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [https://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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/DBPA_ECOLI DBPA_ECOLI]] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965]<ref>PMID:11350034</ref> <ref>PMID:11574482</ref> <ref>PMID:15910005</ref> <ref>PMID:18237742</ref> <ref>PMID:19734347</ref> <ref>PMID:20160110</ref> <ref>PMID:8253085</ref> <ref>PMID:9016593</ref> <ref>PMID:9836593</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The adenosine triphosphate (ATP)-dependent DEAD-box RNA helicase DbpA from Escherichia coli functions in ribosome biogenesis. DbpA is targeted to the nascent 50S subunit by an ancillary, carboxyl-terminal RNA recognition motif (RRM) that specifically binds to hairpin 92 (HP92) of the 23S ribosomal RNA (rRNA). The interaction between HP92 and the RRM is required for the helicase activity of the RecA-like core domains of DbpA. Here, we elucidate the structural basis by which DbpA activity is endorsed when the enzyme interacts with the maturing ribosome. We used nuclear magnetic resonance (NMR) spectroscopy to show that the RRM and the carboxyl-terminal RecA-like domain tightly interact. This orients HP92 such that this RNA hairpin can form electrostatic interactions with a positively charged patch in the N-terminal RecA-like domain. Consequently, the enzyme can stably adopt the catalytically important, closed conformation. The substrate binding mode in this complex reveals that a region 5' to helix 90 in the maturing ribosome is specifically targeted by DbpA. Finally, our results indicate that the ribosome maturation defects induced by a dominant negative DbpA mutation are caused by a delayed dissociation of DbpA from the nascent ribosome. Taken together, our findings provide unique insights into the important regulatory mechanism that modulates the activity of DbpA.

			Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome.,Wurm JP, Glowacz KA, Sprangers R Proc Natl Acad Sci U S A. 2021 Aug 31;118(35). pii: 2105961118. doi:, 10.1073/pnas.2105961118. PMID:34453003<ref>PMID:34453003</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7bbb" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Helicase 3D structures\|Helicase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Sprangers R]]		[[Category: RNA helicase]]
	[[Category: Wurm JP]]		[[Category: Sprangers, R]]
			[[Category: Wurm, J P]]
			[[Category: Dead box helicase]]
			[[Category: Ribosome biogenesis]]
			[[Category: Rna]]
			[[Category: Rna binding protein]]

OCA at 09:51, 14 July 2021

2021-07-14T09:51:11Z

← Older revision		Revision as of 09:51, 14 July 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7bbb is ~~ON HOLD until Paper Publication~~		==Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA==
			<StructureSection load='7bbb' size='340' side='right'caption='[[7bbb]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BBB FirstGlance]. <br>
	~~Description~~:		</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=7bbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bbb OCA], [https://pdbe.org/7bbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bbb RCSB], [https://www.ebi.ac.uk/pdbsum/7bbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bbb ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Sprangers R]]
			[[Category: Wurm JP]]

OCA at 06:35, 20 January 2021

2021-01-20T06:35:06Z

← Older revision		Revision as of 06:35, 20 January 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7bbb is ON HOLD		The entry 7bbb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7bbb" [edit=sysop:move=sysop]

2020-12-24T07:49:32Z

Protected "7bbb" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:49, 24 December 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7bbb is ON HOLD Authors: Description: Category: Unreleased Structures

2020-12-24T07:49:30Z

New page: '''Unreleased structure''' The entry 7bbb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7bbb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]