8amd - Revision history

OCA at 06:40, 3 July 2025

2025-07-03T06:40:21Z

← Older revision		Revision as of 06:40, 3 July 2025
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8amd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8amd OCA], [https://pdbe.org/8amd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8amd RCSB], [https://www.ebi.ac.uk/pdbsum/8amd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8amd 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=8amd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8amd OCA], [https://pdbe.org/8amd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8amd RCSB], [https://www.ebi.ac.uk/pdbsum/8amd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8amd ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/A0A0B7KZM2_STREE A0A0B7KZM2_STREE] Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.[HAMAP-Rule:MF_00268]

	==See Also==		==See Also==

OCA at 09:40, 14 February 2024

2024-02-14T09:40:00Z

← Older revision		Revision as of 09:40, 14 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8amd]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.] and [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[8amd]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.] and [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.9Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></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=8amd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8amd OCA], [https://pdbe.org/8amd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8amd RCSB], [https://www.ebi.ac.uk/pdbsum/8amd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8amd 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=8amd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8amd OCA], [https://pdbe.org/8amd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8amd RCSB], [https://www.ebi.ac.uk/pdbsum/8amd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8amd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A0B7KZM2_STREE A0A0B7KZM2_STREE] Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.[HAMAP-Rule:MF_00268]		[https://www.uniprot.org/uniprot/A0A0B7KZM2_STREE A0A0B7KZM2_STREE] Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.[HAMAP-Rule:MF_00268]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	RecA-mediated homologous recombination (HR) is a key mechanism for genome maintenance and plasticity in bacteria. It proceeds through RecA assembly into a dynamic filament on ssDNA, the presynaptic filament, which mediates DNA homology search and ordered DNA strand exchange. Here, we combined structural, single molecule and biochemical approaches to characterize the ATP-dependent assembly mechanism of the presynaptic filament of RecA from Streptococcus pneumoniae (SpRecA), in comparison to the Escherichia coli RecA (EcRecA) paradigm. EcRecA polymerization on ssDNA is assisted by the Single-Stranded DNA Binding (SSB) protein, which unwinds ssDNA secondary structures that block EcRecA nucleofilament growth. We report by direct microscopic analysis of SpRecA filamentation on ssDNA that neither of the two paralogous pneumococcal SSBs could assist the extension of SpRecA nucleopolymers. Instead, we found that the conserved RadA helicase promotes SpRecA nucleofilamentation in an ATP-dependent manner. This allowed us to solve the atomic structure of such a long native SpRecA nucleopolymer by cryoEM stabilized with ATPgammaS. It was found to be equivalent to the crystal structure of the EcRecA filament with a marked difference in how RecA mediates nucleotide orientation in the stretched ssDNA. Then, our results show that SpRecA and EcRecA HR activities are different, in correlation with their distinct ATP-dependent ssDNA binding modes.

	Assembly mechanism and cryoEM structure of RecA recombination nucleofilaments from Streptococcus pneumoniae.,Hertzog M, Perry TN, Dupaigne P, Serres S, Morales V, Soulet AL, Bell JC, Margeat E, Kowalczykowski SC, Le Cam E, Fronzes R, Polard P Nucleic Acids Res. 2023 Feb 21:gkad080. doi: 10.1093/nar/gkad080. PMID:36806960<ref>PMID:36806960</ref>		==See Also==
			*[[3D structures of recombinase A\|3D structures of recombinase A]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 8amd" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:20, 22 March 2023

2023-03-22T07:20:40Z

← Older revision		Revision as of 07:20, 22 March 2023
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	~~'''Unreleased structure'''~~

	~~The entry~~ 8amd is ~~ON HOLD until Paper~~ Publication		==Cryo-EM structure of the RecA presynaptic filament from S.pneumoniae==
			<StructureSection load='8amd' size='340' side='right'caption='[[8amd]], [[Resolution\|resolution]] 3.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8amd]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.] and [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMD FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene></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=8amd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8amd OCA], [https://pdbe.org/8amd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8amd RCSB], [https://www.ebi.ac.uk/pdbsum/8amd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8amd ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/A0A0B7KZM2_STREE A0A0B7KZM2_STREE] Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage.[HAMAP-Rule:MF_00268]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			RecA-mediated homologous recombination (HR) is a key mechanism for genome maintenance and plasticity in bacteria. It proceeds through RecA assembly into a dynamic filament on ssDNA, the presynaptic filament, which mediates DNA homology search and ordered DNA strand exchange. Here, we combined structural, single molecule and biochemical approaches to characterize the ATP-dependent assembly mechanism of the presynaptic filament of RecA from Streptococcus pneumoniae (SpRecA), in comparison to the Escherichia coli RecA (EcRecA) paradigm. EcRecA polymerization on ssDNA is assisted by the Single-Stranded DNA Binding (SSB) protein, which unwinds ssDNA secondary structures that block EcRecA nucleofilament growth. We report by direct microscopic analysis of SpRecA filamentation on ssDNA that neither of the two paralogous pneumococcal SSBs could assist the extension of SpRecA nucleopolymers. Instead, we found that the conserved RadA helicase promotes SpRecA nucleofilamentation in an ATP-dependent manner. This allowed us to solve the atomic structure of such a long native SpRecA nucleopolymer by cryoEM stabilized with ATPgammaS. It was found to be equivalent to the crystal structure of the EcRecA filament with a marked difference in how RecA mediates nucleotide orientation in the stretched ssDNA. Then, our results show that SpRecA and EcRecA HR activities are different, in correlation with their distinct ATP-dependent ssDNA binding modes.

	~~Authors:~~ Perry, ~~T.N.~~, Fronzes, R., Polard, P.~~, Hertzog, M~~.		Assembly mechanism and cryoEM structure of RecA recombination nucleofilaments from Streptococcus pneumoniae.,Hertzog M, Perry TN, Dupaigne P, Serres S, Morales V, Soulet AL, Bell JC, Margeat E, Kowalczykowski SC, Le Cam E, Fronzes R, Polard P Nucleic Acids Res. 2023 Feb 21:gkad080. doi: 10.1093/nar/gkad080. PMID:36806960<ref>PMID:36806960</ref>

	~~Description: Cryo-EM structure~~ of the ~~RecA presynaptic filament from~~ S.~~pneumoniae~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Fronzes, R]]		<div class="pdbe-citations 8amd" style="background-color:#fffaf0;"></div>
	[[Category: ~~Polard, P~~]]		== References ==
	[[Category: Perry~~, T.N~~]]		<references/>
	[[Category: ~~Hertzog, M~~]]		__TOC__
			</StructureSection>
			[[Category: Bacteriophage sp]]
			[[Category: Large Structures]]
			[[Category: Streptococcus pneumoniae]]
			[[Category: Fronzes R]]
			[[Category: Hertzog M]]
			[[Category: Perry TN]]
			[[Category: Polard P]]

OCA at 16:36, 19 October 2022

2022-10-19T16:36:51Z

← Older revision		Revision as of 16:36, 19 October 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8amd is ON HOLD		The entry 8amd is ON HOLD until Paper Publication

	Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.		Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.

OCA at 06:27, 21 September 2022

2022-09-21T06:27:03Z

← Older revision		Revision as of 06:27, 21 September 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8amd is ON HOLD ~~until sometime in the future~~		The entry 8amd is ON HOLD

	Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.		Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Fronzes, R]]		[[Category: Fronzes, R]]
			[[Category: Polard, P]]
	[[Category: Perry, T.N]]		[[Category: Perry, T.N]]
	[[Category: Hertzog, M]]		[[Category: Hertzog, M]]
	~~[[Category: Polard, P]]~~

OCA at 03:47, 18 August 2022

2022-08-18T03:47:21Z

← Older revision		Revision as of 03:47, 18 August 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8amd is ON HOLD		The entry 8amd is ON HOLD until sometime in the future

	Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.		Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Fronzes, R]]		[[Category: Fronzes, R]]
	~~[[Category: Polard, P]]~~
	[[Category: Perry, T.N]]		[[Category: Perry, T.N]]
	[[Category: Hertzog, M]]		[[Category: Hertzog, M]]
			[[Category: Polard, P]]

OCA: Protected "8amd" [edit=sysop:move=sysop]

2022-08-10T03:57:43Z

Protected "8amd" [edit=sysop:move=sysop]

← Older revision	Revision as of 03:57, 10 August 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8amd is ON HOLD Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M. Description: Cryo-EM structure of the RecA presynaptic filament from S.p...

2022-08-10T03:57:42Z

New page: '''Unreleased structure''' The entry 8amd is ON HOLD Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M. Description: Cryo-EM structure of the RecA presynaptic filament from S.p...

New page

'''Unreleased structure'''

The entry 8amd is ON HOLD

Authors: Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.

Description: Cryo-EM structure of the RecA presynaptic filament from S.pneumoniae
[[Category: Unreleased Structures]]
[[Category: Fronzes, R]]
[[Category: Polard, P]]
[[Category: Perry, T.N]]
[[Category: Hertzog, M]]