5x4i - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:45 GMT

←Older revision		Revision as of 07:53, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5x4i' size='340' side='right'caption='[[5x4i]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5x4i' size='340' side='right'caption='[[5x4i]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x4i]] 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=5X4I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x4i]] 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=5X4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X4I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.092Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5x4h\|5x4h]]~~, ~~[[5x4j\|5x4j]], [[5x4k\|5x4k]]~~<~~/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=5x4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4i OCA], [https://pdbe.org/5x4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x4i RCSB], [https://www.ebi.ac.uk/pdbsum/5x4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4i ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PF2055 ([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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5x4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4i OCA], [~~http~~://pdbe.org/5x4i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x4i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x4i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8TZE0_PYRFU Q8TZE0_PYRFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Chen~~, J N~~]]	+	[[Category: Chen JN]]
-	[[Category: He~~, J H~~]]	+	[[Category: He JH]]
-	[[Category: Li~~, M J~~]]	+	[[Category: Li MJ]]
-	[[Category: Liu~~, X P~~]]	+	[[Category: Liu XP]]
-	[[Category: Wang~~, F P~~]]	+	[[Category: Wang FP]]
-	[[Category: Xiao, X]]	+	[[Category: Xiao X]]
-	[[Category: Xu~~, C Y~~]]	+	[[Category: Xu CY]]
-	[[Category: Yi~~, G S~~]]	+	[[Category: Yi GS]]
-	[[Category: Yu, F]]	+	[[Category: Yu F]]
-	[[Category: Zhou, H]]	+	[[Category: Zhou H]]
-	~~[[Category: Archaeal recj]]~~	+
-	~~[[Category: Cmg interaction domain]]~~	+
-	~~[[Category: Gin]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Interaction]]~~	+
-	~~[[Category: Nuclease activity~~]]	+

OCA at 09:12, 18 December 2019

OCA — Wed, 18 Dec 2019 09:12:55 GMT

←Older revision		Revision as of 09:12, 18 December 2019
Line 1:		Line 1:

	==Pyrococcus furiosus RecJ (D83A, Mn-soaking)==		==Pyrococcus furiosus RecJ (D83A, Mn-soaking)==
-	<StructureSection load='5x4i' size='340' side='right' caption='[[5x4i]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5x4i' size='340' side='right'caption='[[5x4i]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x4i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x4i]] 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=5X4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4h\|5x4h]], [[5x4j\|5x4j]], [[5x4k\|5x4k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4h\|5x4h]], [[5x4j\|5x4j]], [[5x4k\|5x4k]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF2055 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5x4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4i OCA], [http://pdbe.org/5x4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4i RCSB], [http://www.ebi.ac.uk/pdbsum/5x4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4i 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=5x4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4i OCA], [http://pdbe.org/5x4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4i RCSB], [http://www.ebi.ac.uk/pdbsum/5x4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4i ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RecJ nucleases specifically degrade single-stranded (ss) DNA in the 5' to 3' direction. Archaeal RecJ is different from bacterial RecJ in sequence, domain organization, and substrate specificity. The RecJ from archaea Pyrococcus furiosus (PfuRecJ) also hydrolyzes RNA strands in the 3' to 5' direction. Like eukaryotic Cdc45 protein, archaeal RecJ forms a complex with MCM helicase and GINS. Here, we report the crystal structures of PfuRecJ and the complex of PfuRecJ and two CMPs. PfuRecJ bind one or two divalent metal ions in its crystal structure. A channel consisting of several positively charged residues is identified in the complex structure, and might be responsible for binding substrate ssDNA and/or releasing single nucleotide products. The deletion of the complex interaction domain (CID) increases the values of kcat/Km of 5' exonuclease activity on ssDNA and 3' exonuclease activity on ssRNA by 5- and 4-fold, respectively, indicating that the CID functions as a regulator of enzymatic activity. The DHH domain of PfuRecJ interacts with the C-terminal beta-sheet domain of the GINS51 subunit in the tetrameric GINS complex. The relationship of archaeal and bacterial RecJs, as well as eukaryotic Cdc45, is discussed based on biochemical and structural results.
		+
		+	The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45.,Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP Nucleic Acids Res. 2017 Dec 1;45(21):12551-12564. doi: 10.1093/nar/gkx887. PMID:30053256<ref>PMID:30053256</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x4i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrfu]]
	[[Category: Chen, J N]]		[[Category: Chen, J N]]
	[[Category: He, J H]]		[[Category: He, J H]]

OCA at 06:29, 15 February 2018

OCA — Thu, 15 Feb 2018 06:29:31 GMT

←Older revision		Revision as of 06:29, 15 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x4i ~~is ON HOLD until Feb 13 2019~~	+	==Pyrococcus furiosus RecJ (D83A, Mn-soaking)==
-		+	<StructureSection load='5x4i' size='340' side='right' caption='[[5x4i]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~Authors~~: ~~Li, M~~.J.~~, Yi, G~~.S.~~, Yu, F~~., ~~Zhou~~, H., ~~Chen, J~~.N., Xu, C.Y., ~~Wang, F~~.P., ~~Xiao, X~~., He, J.H., Liu, X.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x4i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X4I FirstGlance]. <br>
-	~~Description~~: ~~Pyrococcus furiosus RecJ (D83A~~, ~~Mn-soaking)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x4h\|5x4h]], [[5x4j\|5x4j]], [[5x4k\|5x4k]]</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=5x4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x4i OCA], [http://pdbe.org/5x4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x4i RCSB], [http://www.ebi.ac.uk/pdbsum/5x4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x4i ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, J N]]
		+	[[Category: He, J H]]
		+	[[Category: Li, M J]]
		+	[[Category: Liu, X P]]
		+	[[Category: Wang, F P]]
		+	[[Category: Xiao, X]]
		+	[[Category: Xu, C Y]]
		+	[[Category: Yi, G S]]
		+	[[Category: Yu, F]]
	[[Category: Zhou, H]]		[[Category: Zhou, H]]
-	[[Category: ~~He, J.H~~]]	+	[[Category: Archaeal recj]]
-	[[Category: ~~Yi, G.S~~]]	+	[[Category: Cmg interaction domain]]
-	[[Category: ~~Li, M.J~~]]	+	[[Category: Gin]]
-	[[Category: ~~Chen, J.N~~]]	+	[[Category: Hydrolase]]
-	[[Category: ~~Liu, X.P~~]]	+	[[Category: Interaction]]
-	[[Category: ~~Wang, F.P]]~~	+	[[Category: Nuclease activity]]
-	~~[[Category: Yu, F]]~~	+
-	~~[[Category: Xiao, X]]~~	+
-	~~[[Category: Xu, C.Y~~]]	+

OCA at 15:16, 27 September 2017

OCA — Wed, 27 Sep 2017 15:16:19 GMT

←Older revision		Revision as of 15:16, 27 September 2017
Line 7:		Line 7:
	Description: Pyrococcus furiosus RecJ (D83A, Mn-soaking)		Description: Pyrococcus furiosus RecJ (D83A, Mn-soaking)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wang, F.P]]
	[[Category: Zhou, H]]		[[Category: Zhou, H]]
	[[Category: He, J.H]]		[[Category: He, J.H]]
-	[[Category: Yu, F]]
	[[Category: Yi, G.S]]		[[Category: Yi, G.S]]
	[[Category: Li, M.J]]		[[Category: Li, M.J]]
	[[Category: Chen, J.N]]		[[Category: Chen, J.N]]
-	[[Category: Xiao, X]]
	[[Category: Liu, X.P]]		[[Category: Liu, X.P]]
		+	[[Category: Wang, F.P]]
		+	[[Category: Yu, F]]
		+	[[Category: Xiao, X]]
	[[Category: Xu, C.Y]]		[[Category: Xu, C.Y]]

OCA at 20:10, 15 March 2017

OCA — Wed, 15 Mar 2017 20:10:23 GMT

←Older revision		Revision as of 20:10, 15 March 2017
Line 7:		Line 7:
	Description: Pyrococcus furiosus RecJ (D83A, Mn-soaking)		Description: Pyrococcus furiosus RecJ (D83A, Mn-soaking)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Wang, F.P]]
	[[Category: Zhou, H]]		[[Category: Zhou, H]]
	[[Category: He, J.H]]		[[Category: He, J.H]]
		+	[[Category: Yu, F]]
	[[Category: Yi, G.S]]		[[Category: Yi, G.S]]
	[[Category: Li, M.J]]		[[Category: Li, M.J]]
	[[Category: Chen, J.N]]		[[Category: Chen, J.N]]
-	[[Category: Liu, X.P]]
-	[[Category: Wang, F.P]]
-	[[Category: Yu, F]]
	[[Category: Xiao, X]]		[[Category: Xiao, X]]
		+	[[Category: Liu, X.P]]
	[[Category: Xu, C.Y]]		[[Category: Xu, C.Y]]

OCA: Protected "5x4i" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:44:37 GMT

Protected "5x4i" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:44, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x4i is ON HOLD until Feb 13 2019 Authors: Li, M.J., Yi, G.S., Yu, F., Zhou, H., Chen, J.N., Xu, C.Y., Wang, F.P., Xiao, X., He, J.H., Liu, X.P. De...

OCA — Thu, 09 Mar 2017 15:44:36 GMT

New page: '''Unreleased structure''' The entry 5x4i is ON HOLD until Feb 13 2019 Authors: Li, M.J., Yi, G.S., Yu, F., Zhou, H., Chen, J.N., Xu, C.Y., Wang, F.P., Xiao, X., He, J.H., Liu, X.P. De...

New page

'''Unreleased structure'''

The entry 5x4i is ON HOLD until Feb 13 2019

Authors: Li, M.J., Yi, G.S., Yu, F., Zhou, H., Chen, J.N., Xu, C.Y., Wang, F.P., Xiao, X., He, J.H., Liu, X.P.

Description: Pyrococcus furiosus RecJ (D83A, Mn-soaking)
[[Category: Unreleased Structures]]
[[Category: Zhou, H]]
[[Category: He, J.H]]
[[Category: Yi, G.S]]
[[Category: Li, M.J]]
[[Category: Chen, J.N]]
[[Category: Liu, X.P]]
[[Category: Wang, F.P]]
[[Category: Yu, F]]
[[Category: Xiao, X]]
[[Category: Xu, C.Y]]