4yov - Revision history

OCA at 09:03, 20 March 2024

OCA — Wed, 20 Mar 2024 09:03:57 GMT

←Older revision		Revision as of 09:03, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YOV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YOV 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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [https://pdbe.org/4yov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [https://www.ebi.ac.uk/pdbsum/4yov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yov ProSAT]</span></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]] 2.05Å</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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [https://pdbe.org/4yov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [https://www.ebi.ac.uk/pdbsum/4yov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yov ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A060P168_PYRHR A0A060P168_PYRHR]		[https://www.uniprot.org/uniprot/A0A060P168_PYRHR A0A060P168_PYRHR]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site approximately 9 A away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.
-
-	Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.,Miyazono KI, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M Nucleic Acids Res. 2015 Jul 2. pii: gkv654. PMID:26138487<ref>PMID:26138487</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4yov" style="background-color:#fffaf0;"></div>

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

OCA at 08:23, 3 May 2023

OCA — Wed, 03 May 2023 08:23:29 GMT

←Older revision		Revision as of 08:23, 3 May 2023
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	<StructureSection load='4yov' size='340' side='right'caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='4yov' size='340' side='right'caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~'pyrococcus_shinkaii' 'pyrococcus shinkaii'~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YOV FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [https://pdbe.org/4yov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [https://www.ebi.ac.uk/pdbsum/4yov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yov 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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [~~http~~://pdbe.org/4yov PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yov PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yov ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A060P168_PYRHR A0A060P168_PYRHR]
	<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 shinkaii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ito, T~~]]	+	[[Category: Pyrococcus horikoshii]]
-	[[Category: ~~Miyazono, K~~]]	+	[[Category: Unidentified]]
-	[[Category: ~~Tanokura, M~~]]	+	[[Category: Ito T]]
-	[[Category: ~~Exonuclease~~]]	+	[[Category: Miyazono K]]
-	[[Category: ~~Hydrolase-dna complex~~]]	+	[[Category: Tanokura M]]

OCA at 08:47, 5 February 2020

OCA — Wed, 05 Feb 2020 08:47:22 GMT

←Older revision		Revision as of 08:47, 5 February 2020
Line 1:		Line 1:

	==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA==		==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA==
-	<StructureSection load='4yov' size='340' side='right' caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='4yov' size='340' side='right'caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4yov" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yov" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus shinkaii]]		[[Category: Pyrococcus shinkaii]]
		+	[[Category: Large Structures]]
	[[Category: Ito, T]]		[[Category: Ito, T]]
	[[Category: Miyazono, K]]		[[Category: Miyazono, K]]

OCA at 17:54, 16 November 2017

OCA — Thu, 16 Nov 2017 17:54:24 GMT

←Older revision		Revision as of 17:54, 16 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA==		==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA==
	<StructureSection load='4yov' size='340' side='right' caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='4yov' size='340' side='right' caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [http://pdbe.org/4yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [http://www.ebi.ac.uk/pdbsum/4yov 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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [http://pdbe.org/4yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [http://www.ebi.ac.uk/pdbsum/4yov PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yov ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus shinkaii]]
	[[Category: Ito, T]]		[[Category: Ito, T]]
	[[Category: Miyazono, K]]		[[Category: Miyazono, K]]

OCA at 07:22, 30 September 2015

OCA — Wed, 30 Sep 2015 07:22:14 GMT

←Older revision		Revision as of 07:22, 30 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [http://www.ebi.ac.uk/pdbsum/4yov 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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [http://pdbe.org/4yov PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [http://www.ebi.ac.uk/pdbsum/4yov PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 4yov" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:19, 15 July 2015

OCA — Wed, 15 Jul 2015 13:19:18 GMT

←Older revision		Revision as of 13:19, 15 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dA==
		+	<StructureSection load='4yov' size='340' side='right' caption='[[4yov]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yov]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YOV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YOV FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yor\|4yor]], [[4yot\|4yot]], [[4you\|4you]], [[4yow\|4yow]], [[4yox\|4yox]], [[4yoy\|4yoy]]</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=4yov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yov OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yov RCSB], [http://www.ebi.ac.uk/pdbsum/4yov PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleases play important roles in nucleic acid processes, such as replication, repair and recombination. Recently, we identified a novel single-strand specific 3'-5' exonuclease, PfuExo I, from the hyperthermophilic archaeon Pyrococcus furiosus, which may be involved in the Thermococcales-specific DNA repair system. PfuExo I forms a trimer and cleaves single-stranded DNA at every two nucleotides. Here, we report the structural basis for the cleavage mechanism of this novel exonuclease family. A structural analysis of PhoExo I, the homologous enzyme from P. horikoshii OT3, showed that PhoExo I utilizes an RNase H-like active site and possesses a 3'-OH recognition site approximately 9 A away from the active site, which enables cleavage at every two nucleotides. Analyses of the heterotrimeric and monomeric PhoExo I activities showed that trimerization is indispensable for its processive cleavage mechanism, but only one active site of the trimer is required.

-	~~The entry 4yov is ON HOLD until Paper Publication~~	+	Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I.,Miyazono KI, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M Nucleic Acids Res. 2015 Jul 2. pii: gkv654. PMID:26138487<ref>PMID:26138487</ref>

-	~~Authors: Miyazono~~, K.~~, Ito, T~~.~~, Tanokura, M~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Ito, T]]		[[Category: Ito, T]]
	[[Category: Miyazono, K]]		[[Category: Miyazono, K]]
	[[Category: Tanokura, M]]		[[Category: Tanokura, M]]
		+	[[Category: Exonuclease]]
		+	[[Category: Hydrolase-dna complex]]

OCA at 11:44, 1 April 2015

OCA — Wed, 01 Apr 2015 11:44:36 GMT

←Older revision		Revision as of 11:44, 1 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yov is ON HOLD	+	The entry 4yov is ON HOLD until Paper Publication

	Authors: Miyazono, K., Ito, T., Tanokura, M.		Authors: Miyazono, K., Ito, T., Tanokura, M.

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

OCA — Wed, 18 Mar 2015 10:58:46 GMT

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

←Older revision

Revision as of 10:58, 18 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yov is ON HOLD Authors: Miyazono, K., Ito, T., Tanokura, M. Description: Category: Unreleased Structures Category: Ito, T [[Category: Miy...

OCA — Wed, 18 Mar 2015 10:58:44 GMT

New page: '''Unreleased structure''' The entry 4yov is ON HOLD Authors: Miyazono, K., Ito, T., Tanokura, M. Description: Category: Unreleased Structures Category: Ito, T [[Category: Miy...

New page

'''Unreleased structure'''

The entry 4yov is ON HOLD

Authors: Miyazono, K., Ito, T., Tanokura, M.

Description:
[[Category: Unreleased Structures]]
[[Category: Ito, T]]
[[Category: Miyazono, K]]
[[Category: Tanokura, M]]