4wa8 - Revision history

OCA at 07:29, 27 September 2023

OCA — Wed, 27 Sep 2023 07:29:19 GMT

←Older revision		Revision as of 07:29, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri_AV19 Methanopyrus kandleri AV19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri_AV19 Methanopyrus kandleri AV19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WA8 FirstGlance]. <br>
-	</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></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]] 2.2Å</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></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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [https://pdbe.org/4wa8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [https://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [https://pdbe.org/4wa8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [https://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:59, 7 April 2023

OCA — Fri, 07 Apr 2023 06:59:13 GMT

←Older revision		Revision as of 06:59, 7 April 2023
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	<StructureSection load='4wa8' size='340' side='right'caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4wa8' size='340' side='right'caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metka Metka~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri_AV19 Methanopyrus kandleri AV19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WA8 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>~~</td></tr>~~	+	</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></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fen, MK0566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190192 METKA])~~</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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [https://pdbe.org/4wa8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [https://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [~~http~~://pdbe.org/4wa8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FEN_METKA FEN_METKA]] Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).	+	[https://www.uniprot.org/uniprot/FEN_METKA FEN_METKA] Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metka~~]]	+	[[Category: Methanopyrus kandleri AV19]]
-	[[Category: Dunten, P]]	+	[[Category: Dunten P]]
-	[[Category: Horton~~, N C~~]]	+	[[Category: Horton NC]]
-	[[Category: Shah, S]]	+	[[Category: Shah S]]
-	~~[[Category: Dna nuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nucleotide excision repair~~]]	+

OCA at 08:12, 23 May 2019

OCA — Thu, 23 May 2019 08:12:53 GMT

←Older revision		Revision as of 08:12, 23 May 2019
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	==Methanopyrus Kandleri FEN-1 nuclease==		==Methanopyrus Kandleri FEN-1 nuclease==
-	<StructureSection load='4wa8' size='340' side='right' caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4wa8' size='340' side='right'caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metka Metka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WA8 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fen, MK0566 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190192 METKA])</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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://pdbe.org/4wa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://pdbe.org/4wa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 ProSAT]</span></td></tr>
	</table>		</table>
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Metka]]
	[[Category: Dunten, P]]		[[Category: Dunten, P]]
	[[Category: Horton, N C]]		[[Category: Horton, N C]]

OCA at 20:43, 11 August 2016

OCA — Thu, 11 Aug 2016 20:43:51 GMT

←Older revision		Revision as of 20:43, 11 August 2016
Line 1:		Line 1:
		+
	==Methanopyrus Kandleri FEN-1 nuclease==		==Methanopyrus Kandleri FEN-1 nuclease==
	<StructureSection load='4wa8' size='340' side='right' caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4wa8' size='340' side='right' caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WA8 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></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></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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://pdbe.org/4wa8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wa8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4wa8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:32, 24 December 2014

OCA — Wed, 24 Dec 2014 11:32:13 GMT

←Older revision		Revision as of 11:32, 24 December 2014
Line 6:		Line 6:
	<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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FEN_METKA FEN_METKA]] Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:03, 12 November 2014

OCA — Wed, 12 Nov 2014 07:03:55 GMT

←Older revision		Revision as of 07:03, 12 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Methanopyrus Kandleri FEN-1 nuclease==
		+	<StructureSection load='4wa8' size='340' side='right' caption='[[4wa8]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4wa8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WA8 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></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=4wa8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wa8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wa8 RCSB], [http://www.ebi.ac.uk/pdbsum/4wa8 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA repair is fundamental to genome stability and is found in all three domains of life. However, many archaeal species, such as Methanopyrus kandleri, contain only a subset of the eukaryotic nucleotide excision repair (NER) homologues, and those present often contain significant differences compared to their eukaryotic homologues. To clarify the role of the NER XPG-like protein Mk0566 from M. kandleri, its biochemical activity and three dimensional structure were investigated. Both were found to be more similar to human FEN-1 than human XPG, suggesting a biological role in replication and long-patch base excision repair rather than in NER. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.

-	~~The entry 4wa8 is ON HOLD until Paper Publication~~	+	Structure and Specificity of FEN-1 from Methanopyrus kandleri.,Shah S, Dunten P, Stiteler A, Park CK, Horton NC Proteins. 2014 Oct 30. doi: 10.1002/prot.24704. PMID:25354467<ref>PMID:25354467</ref>

-	~~Authors: Shah~~, S., Dunten, P., Horton, N.C.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Methanopyrus Kandleri FEN-1~~ nuclease	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dunten, P]]
		+	[[Category: Horton, N C]]
		+	[[Category: Shah, S]]
		+	[[Category: Dna nuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nucleotide excision repair]]

OCA at 08:53, 10 September 2014

OCA — Wed, 10 Sep 2014 08:53:01 GMT

←Older revision		Revision as of 08:53, 10 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4wa8 is ON HOLD	+	The entry 4wa8 is ON HOLD until Paper Publication

	Authors: Shah, S., Dunten, P., Horton, N.C.		Authors: Shah, S., Dunten, P., Horton, N.C.

	Description: Methanopyrus Kandleri FEN-1 nuclease		Description: Methanopyrus Kandleri FEN-1 nuclease

OCA: Protected "4wa8" [edit=sysop:move=sysop]

OCA — Thu, 04 Sep 2014 04:52:02 GMT

Protected "4wa8" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 4 September 2014

OCA: New page: '''Unreleased structure''' The entry 4wa8 is ON HOLD Authors: Shah, S., Dunten, P., Horton, N.C. Description: Methanopyrus Kandleri FEN-1 nuclease

OCA — Thu, 04 Sep 2014 04:52:00 GMT

New page: '''Unreleased structure''' The entry 4wa8 is ON HOLD Authors: Shah, S., Dunten, P., Horton, N.C. Description: Methanopyrus Kandleri FEN-1 nuclease

New page

'''Unreleased structure'''

The entry 4wa8 is ON HOLD

Authors: Shah, S., Dunten, P., Horton, N.C.

Description: Methanopyrus Kandleri FEN-1 nuclease