4e2t - Revision history

OCA at 14:50, 14 March 2024

2024-03-14T14:50:27Z

← Older revision		Revision as of 14:50, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E2T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.75Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [https://pdbe.org/4e2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [https://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t 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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [https://pdbe.org/4e2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [https://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/RADA_PYRHO RADA_PYRHO]] 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 (By similarity).		[https://www.uniprot.org/uniprot/RADA_PYRHO RADA_PYRHO] 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 (By similarity).
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	In protein splicing, an intervening protein sequence (intein) in the host protein excises itself out and ligates two split host protein sequences (exteins) to produce a mature host protein. Inteins require the involvement for the splicing of the first residue of the extein that follows the intein (which is Cys, Ser, or Thr). Other extein residues near the splicing junctions could modulate splicing efficiency even when they are not directly involved in catalysis. Mutual interdependence between this molecular parasite (intein) and its host protein (exteins) is not beneficial for intein spread but could be advantageous for intein survival during evolution. Elucidating extein-intein dependency has increasingly become important since inteins are recognized as useful biotechnological tools for protein ligation. We determined the structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidated the structural basis for its high efficiency and directed our efforts of engineering that led to rational design of a functional minimized RadA intein. The crystal structure of the minimized RadA intein also revealed the precise interactions between N-extein and the intein. We systematically analyzed the effects at the -1 position of N-extein and were able to significantly improve the splicing efficiency of a less robust splicing variant by eliminating the unfavorable extein-intein interactions observed in the structure. This work provides an example of how unveiling structure-function relationships of inteins offer a promising way of improving their properties as better tools for protein engineering.

	NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.,Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwai H J Mol Biol. 2012 Aug 3;421(1):85-99. Epub 2012 May 2. PMID:22560994<ref>PMID:22560994</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e2t" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:46, 28 September 2022

2022-09-28T06:46:48Z

← Older revision		Revision as of 06:46, 28 September 2022
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	==Crystal Structures of RadA intein from Pyrococcus horikoshii==		==Crystal Structures of RadA intein from Pyrococcus horikoshii==
	<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4e2t' size='340' side='right'caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E2T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [https://pdbe.org/4e2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [https://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [~~http~~://pdbe.org/4e2t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/RADA_PYRHO RADA_PYRHO]] 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 (By similarity).		[[https://www.uniprot.org/uniprot/RADA_PYRHO RADA_PYRHO]] 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 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii]]		[[Category: Large Structures]]
	[[Category: Iwai, H]]		[[Category: Pyrococcus horikoshii OT3]]
	[[Category: Kajander, T]]		[[Category: Iwai H]]
	[[Category: Oeemig~~, J S~~]]		[[Category: Kajander T]]
	[[Category: Wlodawer, A]]		[[Category: Oeemig JS]]
	[[Category: Zhou, D]]		[[Category: Wlodawer A]]
	~~[[Category: Hint-fold]]~~		[[Category: Zhou D]]
	~~[[Category: Intein]]~~
	~~[[Category: Unknown function~~]]

OCA at 07:28, 18 October 2016

2016-10-18T07:28:19Z

← Older revision		Revision as of 07:28, 18 October 2016
Line 3:		Line 3:
	<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([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">radA, PH0263 ([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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://pdbe.org/4e2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t 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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://pdbe.org/4e2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t ProSAT]</span></td></tr>
	</table>		</table>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pyrho~~]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Iwai, H]]		[[Category: Iwai, H]]
	[[Category: Kajander, T]]		[[Category: Kajander, T]]

OCA at 22:27, 4 August 2016

2016-08-04T22:27:24Z

← Older revision		Revision as of 22:27, 4 August 2016
Line 1:		Line 1:

	==Crystal Structures of RadA intein from Pyrococcus horikoshii==		==Crystal Structures of RadA intein from Pyrococcus horikoshii==
	<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~53953 Pyrococcus horikoshii~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t 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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://pdbe.org/4e2t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4e2t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pyrococcus horikoshii~~]]		[[Category: Pyrho]]
	[[Category: Iwai, H]]		[[Category: Iwai, H]]
	[[Category: Kajander, T]]		[[Category: Kajander, T]]

OCA at 20:13, 24 December 2014

2014-12-24T20:13:54Z

← Older revision		Revision as of 20:13, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t 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=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RADA_PYRHO RADA_PYRHO]] 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 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Iwai, H.]]		[[Category: Iwai, H]]
	[[Category: Kajander, T.]]		[[Category: Kajander, T]]
	[[Category: Oeemig, J S.]]		[[Category: Oeemig, J S]]
	[[Category: Wlodawer, A.]]		[[Category: Wlodawer, A]]
	[[Category: Zhou, D.]]		[[Category: Zhou, D]]
	[[Category: Hint-fold]]		[[Category: Hint-fold]]
	[[Category: Intein]]		[[Category: Intein]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 08:31, 5 June 2014

2014-06-05T08:31:33Z

← Older revision		Revision as of 08:31, 5 June 2014
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	[[~~Image~~:~~4e2t~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structures of RadA intein from Pyrococcus horikoshii==
			<StructureSection load='4e2t' size='340' side='right' caption='[[4e2t]], [[Resolution\|resolution]] 1.75Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e2t]] is a 2 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=4E2T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2T FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e2u\|4e2u]], [[2lqm\|2lqm]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">radA, PH0263 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2t RCSB], [http://www.ebi.ac.uk/pdbsum/4e2t PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			In protein splicing, an intervening protein sequence (intein) in the host protein excises itself out and ligates two split host protein sequences (exteins) to produce a mature host protein. Inteins require the involvement for the splicing of the first residue of the extein that follows the intein (which is Cys, Ser, or Thr). Other extein residues near the splicing junctions could modulate splicing efficiency even when they are not directly involved in catalysis. Mutual interdependence between this molecular parasite (intein) and its host protein (exteins) is not beneficial for intein spread but could be advantageous for intein survival during evolution. Elucidating extein-intein dependency has increasingly become important since inteins are recognized as useful biotechnological tools for protein ligation. We determined the structures of one of inteins with high splicing efficiency, the RadA intein from Pyrococcus horikoshii (PhoRadA). The solution NMR structure and the crystal structures elucidated the structural basis for its high efficiency and directed our efforts of engineering that led to rational design of a functional minimized RadA intein. The crystal structure of the minimized RadA intein also revealed the precise interactions between N-extein and the intein. We systematically analyzed the effects at the -1 position of N-extein and were able to significantly improve the splicing efficiency of a less robust splicing variant by eliminating the unfavorable extein-intein interactions observed in the structure. This work provides an example of how unveiling structure-function relationships of inteins offer a promising way of improving their properties as better tools for protein engineering.

	~~{{STRUCTURE_4e2t\| PDB=4e2t \| SCENE= }}~~		NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.,Oeemig JS, Zhou D, Kajander T, Wlodawer A, Iwai H J Mol Biol. 2012 Aug 3;421(1):85-99. Epub 2012 May 2. PMID:22560994<ref>PMID:22560994</ref>

	~~===Crystal Structures~~ of ~~RadA intein from Pyrococcus horikoshii===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22560994}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[4e2t]] is a 2 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=4E2T OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:022560994<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Iwai, H.]]		[[Category: Iwai, H.]]

OCA at 06:24, 25 July 2012

2012-07-25T06:24:31Z

← Older revision		Revision as of 06:24, 25 July 2012
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	[[Image:4e2t.~~jpg~~\|left\|200px]]		[[Image:4e2t.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_4e2t", 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_4e2t\| PDB=4e2t \| SCENE= }}		{{STRUCTURE_4e2t\| PDB=4e2t \| SCENE= }}

	===Crystal Structures of RadA intein from Pyrococcus horikoshii===		===Crystal Structures of RadA intein from Pyrococcus horikoshii===

			{{ABSTRACT_PUBMED_22560994}}

	==About this Structure==		==About this Structure==
	[[4e2t]] is a 2 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=4E2T OCA].		[[4e2t]] is a 2 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=4E2T OCA].

			==Reference==
			<ref group="xtra">PMID:022560994</ref><references group="xtra"/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Iwai, H.]]		[[Category: Iwai, H.]]

OCA at 09:23, 16 May 2012

2012-05-16T09:23:19Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:4e2t.jpg|left|200px]]
-The entry 4e2t is ON HOLD  until Paper Publication
+<!--
-Authors: Oeemig, J.S., Zhou, D., Kajander, T., Wlodawer, A., Iwai, H.
+===Crystal Structures of RadA intein from Pyrococcus horikoshii===
-Description: Crystal Structures of RadA intein from Pyrococcus horikoshii

OCA at 08:44, 9 May 2012

2012-05-09T08:44:42Z

← Older revision		Revision as of 08:44, 9 May 2012
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e2t is ON HOLD		The entry 4e2t is ON HOLD until Paper Publication

	Authors: Oeemig, J.S., Zhou, D., Kajander, T., Wlodawer, A., Iwai, H.		Authors: Oeemig, J.S., Zhou, D., Kajander, T., Wlodawer, A., Iwai, H.

	Description: Crystal Structures of RadA intein from Pyrococcus horikoshii		Description: Crystal Structures of RadA intein from Pyrococcus horikoshii

OCA: Protected "4e2t" [edit=sysop:move=sysop]

2012-03-21T07:15:09Z

Protected "4e2t" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:15, 21 March 2012
(No difference)