5jee - Revision history

OCA at 07:47, 7 February 2024

2024-02-07T07:47:57Z

← Older revision		Revision as of 07:47, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JEE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JEE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.49Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [https://pdbe.org/5jee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [https://www.ebi.ac.uk/pdbsum/5jee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee 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=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [https://pdbe.org/5jee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [https://www.ebi.ac.uk/pdbsum/5jee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RADA_PYRFU RADA_PYRFU] Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.		[https://www.uniprot.org/uniprot/RADA_PYRFU RADA_PYRFU] Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. Here, we report an approach that exploits protein engineering to 'humanise' thermophilic archeal surrogate proteins as targets for small molecule inhibitor discovery, and exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. As human RAD51 has proved impossible to produce in a form that is compatible with the requirements of fragment-based drug discovery, we have developed a surrogate protein system using RadA from Pyrococcus furiosus. Using a monomerised RadA as our starting point, we have adopted two parallel and mutually instructive approaches to mimic the human enzyme: firstly by mutating RadA to increase sequence identity with RAD51 in the BRC repeat binding sites, and secondly by generating a chimeric archaeal-human protein. Both approaches generate proteins that interact with a BRC4 repeat with affinity and stoichiometry comparable to human RAD51. Stepwise humanisation has also allowed us to elucidate the determinants of RAD51 binding to BRC repeats and the contributions of key interacting residues to this interaction. These surrogate proteins have enabled the development of biochemical and biophysical assays in our ongoing fragment-based small molecule inhibitor programme and they have allowed us to determine hundreds of liganded structures in support of our structure-guided design process, demonstrating the feasibility and advantages of using archeal surrogates to overcome difficulties in handling human proteins.

	Engineering archeal surrogate systems for the development of protein-protein interaction inhibitors against human RAD51.,Moschetti T, Sharpe T, Fischer G, Marsh ME, Ng H, Morgan M, Scott D, Blundell TL, Venkitaraman A, Skidmore J, Abell C, Hyvonen M J Mol Biol. 2016 Oct 7. pii: S0022-2836(16)30424-7. doi:, 10.1016/j.jmb.2016.10.009. PMID:27725183<ref>PMID:27725183</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5jee" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Resolvase 3D structures\|Resolvase 3D structures]]		*[[Resolvase 3D structures\|Resolvase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:56, 29 March 2023

2023-03-29T06:56:55Z

← Older revision		Revision as of 06:56, 29 March 2023
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	<StructureSection load='5jee' size='340' side='right'caption='[[5jee]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='5jee' size='340' side='right'caption='[[5jee]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JEE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JEE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PF1926 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [https://pdbe.org/5jee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [https://www.ebi.ac.uk/pdbsum/5jee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee ProSAT]</span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [~~http~~://pdbe.org/5jee PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jee PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/RADA_PYRFU RADA_PYRFU]] Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.		[https://www.uniprot.org/uniprot/RADA_PYRFU RADA_PYRFU] Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Pyrfu~~]]		[[Category: Pyrococcus furiosus DSM 3638]]
	[[Category: Abell, C]]		[[Category: Abell C]]
	[[Category: Blundell~~, T L~~]]		[[Category: Blundell TL]]
	[[Category: Fischer, G]]		[[Category: Fischer G]]
	[[Category: Hyvonen, M]]		[[Category: Hyvonen M]]
	[[Category: Marsh, M]]		[[Category: Marsh M]]
	[[Category: Morgan, M]]		[[Category: Morgan M]]
	[[Category: Moschetti, T]]		[[Category: Moschetti T]]
	[[Category: Ng, H]]		[[Category: Ng H]]
	[[Category: Scott, D]]		[[Category: Scott D]]
	[[Category: Sharpe, T]]		[[Category: Sharpe T]]
	[[Category: Skidmore, J]]		[[Category: Skidmore J]]
	[[Category: Venkitaraman, A]]		[[Category: Venkitaraman A]]
	~~[[Category: Dna repair]]~~
	~~[[Category: Fragment based drug design]]~~
	~~[[Category: Humanisation]]~~
	~~[[Category: Hydrolase~~]]

OCA at 07:44, 10 June 2020

2020-06-10T07:44:40Z

← Older revision		Revision as of 07:44, 10 June 2020
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	==Apo-structure of humanised RadA-mutant humRadA26F==		==Apo-structure of humanised RadA-mutant humRadA26F==
	<StructureSection load='5jee' size='340' side='right' caption='[[5jee]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='5jee' size='340' side='right'caption='[[5jee]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=5JEE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jee]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JEE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JEE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [http://pdbe.org/5jee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [http://www.ebi.ac.uk/pdbsum/5jee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee ProSAT]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PF1926 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jee OCA], [http://pdbe.org/5jee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jee RCSB], [http://www.ebi.ac.uk/pdbsum/5jee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jee ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5jee" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jee" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Resolvase 3D structures\|Resolvase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Pyrfu]]
	[[Category: Abell, C]]		[[Category: Abell, C]]
	[[Category: Blundell, T L]]		[[Category: Blundell, T L]]

OCA at 17:32, 19 October 2016

2016-10-19T17:32:46Z

@@ Line 1: / Line 1: @@
-The entry 5jee is ON HOLD  until Paper Publication
+==Apo-structure of humanised RadA-mutant humRadA26F==
-Authors:
+Engineering archeal surrogate systems for the development of protein-protein interaction inhibitors against human RAD51.,Moschetti T, Sharpe T, Fischer G, Marsh ME, Ng H, Morgan M, Scott D, Blundell TL, Venkitaraman A, Skidmore J, Abell C, Hyvonen M J Mol Biol. 2016 Oct 7. pii: S0022-2836(16)30424-7. doi:, 10.1016/j.jmb.2016.10.009. PMID:27725183<ref>PMID:27725183</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>

OCA at 23:16, 12 July 2016

2016-07-12T23:16:11Z

← Older revision		Revision as of 23:16, 12 July 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5jee is ON HOLD		The entry 5jee is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 15:19, 15 May 2016

2016-05-15T15:19:37Z

← Older revision		Revision as of 15:19, 15 May 2016
Line 3:		Line 3:
	The entry 5jee is ON HOLD		The entry 5jee is ON HOLD

	Authors: ~~Fischer, G., Marsh, M., Moschetti, T., Sharpe, T., Scott, D., Morgan, M., Ng, H., Skidmore, J., Venkitaraman, A., Abell, C., Blundell, T.L., Hyvonen, M.~~		Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Ng, H]]~~
	~~[[Category: Hyvonen, M]]~~
	~~[[Category: Abell, C]]~~
	~~[[Category: Morgan, M]]~~
	~~[[Category: Skidmore, J]]~~
	~~[[Category: Blundell, T.L]]~~
	~~[[Category: Fischer, G]]~~
	~~[[Category: Marsh, M]]~~
	~~[[Category: Scott, D]]~~
	~~[[Category: Venkitaraman, A]]~~
	~~[[Category: Moschetti, T]]~~
	~~[[Category: Sharpe, T]]~~

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

2016-05-11T01:55:33Z

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

← Older revision	Revision as of 01:55, 11 May 2016
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5jee is ON HOLD Authors: Fischer, G., Marsh, M., Moschetti, T., Sharpe, T., Scott, D., Morgan, M., Ng, H., Skidmore, J., Venkitaraman, A., Abell, C....

2016-05-11T01:55:32Z

New page: '''Unreleased structure''' The entry 5jee is ON HOLD Authors: Fischer, G., Marsh, M., Moschetti, T., Sharpe, T., Scott, D., Morgan, M., Ng, H., Skidmore, J., Venkitaraman, A., Abell, C....

New page

'''Unreleased structure'''

The entry 5jee is ON HOLD

Authors: Fischer, G., Marsh, M., Moschetti, T., Sharpe, T., Scott, D., Morgan, M., Ng, H., Skidmore, J., Venkitaraman, A., Abell, C., Blundell, T.L., Hyvonen, M.

Description:
[[Category: Unreleased Structures]]
[[Category: Ng, H]]
[[Category: Hyvonen, M]]
[[Category: Abell, C]]
[[Category: Morgan, M]]
[[Category: Skidmore, J]]
[[Category: Blundell, T.L]]
[[Category: Fischer, G]]
[[Category: Marsh, M]]
[[Category: Scott, D]]
[[Category: Venkitaraman, A]]
[[Category: Moschetti, T]]
[[Category: Sharpe, T]]