5g5s - Revision history

OCA at 13:39, 26 July 2023

2023-07-26T13:39:52Z

←Older revision		Revision as of 13:39, 26 July 2023
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	<StructureSection load='5g5s' size='340' side='right'caption='[[5g5s]], [[Resolution\|resolution]] 2.29Å' scene=''>		<StructureSection load='5g5s' size='340' side='right'caption='[[5g5s]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g5s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5G5S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g5s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G5S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.29Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g5t\|5g5t]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [~~http~~://pdbe.org/5g5s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s 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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [https://pdbe.org/5g5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [https://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AGO_METJA AGO_METJA] A DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements. Uses short ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in slicing of the target DNA (tDNA) (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Endonucleolytically cleaves tDNA (the gDNA indicates where to cleave); two major and two minor products are seen which correspond to cleavage sites between nucleotides 9/10, 10/11, 13/14, and 14/15 downstream of the target residue base-paired with the 5'-end of the gDNA (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Efficient guide-dependent tDNA cleavage requires a minimal length of 15 bp and is maximal at 19 bp (PubMed:28319081). Prefers gDNA with 5'-phosphorylated purines and 3'-pyrimidines; changing these bases alters the cleavage activity and patterns (PubMed:28319084). Also has guide-independent activity on tDNA called 'chopping' (PubMed:28319081). Probably a first round of guide-independent activity on an invading plasmid or virus would generate guide DNAs for subsequent, more efficient, guide-dependent degradation of invading nucleic acids (PubMed:28319081). Has no activity on substrate with a mismatch at positions 10 and 11, on ssDNA or RNA, nor on DNA:RNA hybrids (PubMed:24442234). Digests longer (750 bp) dsDNA as well as circular plasmid and naked genomic DNA, but not chromatin, in a guide DNA-independent manner (PubMed:28319081). Addition of endogenous histone A3 protects DNA from cleavage, while cleavage is insensitive to methylation (PubMed:28319081). When plasmid encoding active or mutated protein (Ala-541) is transformed into Sulfolobus acidocaldarius about 25-fold fewer transformants are found with active protein; reduced levels of plasmid are found in wild-type transformed cells. While S.acidocaldarius grows at a similar temperature to M.jannaschii (70 to 80 degrees Celsius) it has very different histone-like proteins, which presumably do not protect against MjAgo (PubMed:28319081). Binds ssDNA, dsDNA and DNA-RNA hybrids; binding is most efficient with dsDNA (PubMed:24442234).<ref>PMID:24442234</ref> <ref>PMID:27741323</ref> <ref>PMID:28319081</ref> <ref>PMID:28319084</ref> <ref>PMID:28319081</ref>
	<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: Atcc 43067]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grohmann, D]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Keegan, R]]	+	[[Category: Grohmann D]]
-	[[Category: Oellig~~, C A~~]]	+	[[Category: Keegan R]]
-	[[Category: Schneider, S]]	+	[[Category: Oellig CA]]
-	[[Category: Willkomm, S]]	+	[[Category: Schneider S]]
-	[[Category: Zander, A]]	+	[[Category: Willkomm S]]
-	~~[[Category: Argonaute]]~~	+	[[Category: Zander A]]
-	~~[[Category: Bacterial defense]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:40, 13 May 2020

2020-05-13T06:40:23Z

←Older revision		Revision as of 06:40, 13 May 2020
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	==Structure of the Argonaute protein from Methanocaldcoccus janaschii==		==Structure of the Argonaute protein from Methanocaldcoccus janaschii==
-	<StructureSection load='5g5s' size='340' side='right' caption='[[5g5s]], [[Resolution\|resolution]] 2.29Å' scene=''>	+	<StructureSection load='5g5s' size='340' side='right'caption='[[5g5s]], [[Resolution\|resolution]] 2.29Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5G5S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g5s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5G5S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g5t\|5g5t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g5t\|5g5t]]</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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [http://pdbe.org/5g5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [http://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s 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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [http://pdbe.org/5g5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [http://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Argonaute\|Argonaute]]	+	*[[Argonaute 3D structures\|Argonaute 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Grohmann, D]]		[[Category: Grohmann, D]]
	[[Category: Keegan, R]]		[[Category: Keegan, R]]

OCA at 07:09, 29 March 2017

2017-03-29T07:09:01Z

←Older revision		Revision as of 07:09, 29 March 2017
Line 8:		Line 8:
	<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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [http://pdbe.org/5g5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [http://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s 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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [http://pdbe.org/5g5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [http://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing1, while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA2,3. Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process4-6. To identify key residues crucial for MjAgo function, we analysed the effect of several MjAgo mutants. We observe that the nature of the 3' and 5' nucleotides in particular, as well as the switch helix, appear to impact MjAgo cleavage activity. In summary, we provide insights into the molecular mechanisms that drive DNA-guided DNA silencing by an archaeal Ago.
		+
		+	Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein.,Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S Nat Microbiol. 2017 Mar 20;2:17035. doi: 10.1038/nmicrobiol.2017.35. PMID:28319084<ref>PMID:28319084</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5g5s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Argonaute\|Argonaute]]		*[[Argonaute\|Argonaute]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:10, 9 March 2017

2017-03-09T07:10:11Z

←Older revision		Revision as of 07:10, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5g5s is ~~ON HOLD until Paper Publication~~	+	==Structure of the Argonaute protein from Methanocaldcoccus janaschii==
		+	<StructureSection load='5g5s' size='340' side='right' caption='[[5g5s]], [[Resolution\|resolution]] 2.29Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5g5s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G5S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g5t\|5g5t]]</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=5g5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5s OCA], [http://pdbe.org/5g5s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g5s RCSB], [http://www.ebi.ac.uk/pdbsum/5g5s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5s ProSAT]</span></td></tr>
		+	</table>

-	~~Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S.~~	+	==See Also==
-		+	*[[Argonaute\|Argonaute]]
-	~~Description: Structure of the Argonaute protein from Methanocaldcoccus janaschii~~	+	__TOC__
-	[[~~Category: Unreleased Structures~~]]	+	</StructureSection>
	[[Category: Grohmann, D]]		[[Category: Grohmann, D]]
		+	[[Category: Keegan, R]]
		+	[[Category: Oellig, C A]]
	[[Category: Schneider, S]]		[[Category: Schneider, S]]
-	[[Category: ~~Oellig~~, ~~C.A~~]]	+	[[Category: Willkomm, S]]
	[[Category: Zander, A]]		[[Category: Zander, A]]
-	[[Category: ~~Keegan, R~~]]	+	[[Category: Argonaute]]
-	[[Category: ~~Willkomm, S~~]]	+	[[Category: Bacterial defense]]
		+	[[Category: Hydrolase]]

OCA at 08:12, 21 September 2016

2016-09-21T08:12:20Z

←Older revision		Revision as of 08:12, 21 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5g5s is ON HOLD	+	The entry 5g5s is ON HOLD until Paper Publication

	Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S.		Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S.

OCA: Protected "5g5s" [edit=sysop:move=sysop]

2016-06-20T11:07:14Z

Protected "5g5s" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:07, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5g5s is ON HOLD Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S. Description: Structure of the Argonaute pr...

2016-06-20T11:07:13Z

New page: '''Unreleased structure''' The entry 5g5s is ON HOLD Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S. Description: Structure of the Argonaute pr...

New page

'''Unreleased structure'''

The entry 5g5s is ON HOLD

Authors: Schneider, S., Oellig, C.A., Keegan, R., Grohmann, D., Zander, A., Willkomm, S.

Description: Structure of the Argonaute protein from Methanocaldcoccus janaschii
[[Category: Unreleased Structures]]
[[Category: Grohmann, D]]
[[Category: Schneider, S]]
[[Category: Oellig, C.A]]
[[Category: Zander, A]]
[[Category: Keegan, R]]
[[Category: Willkomm, S]]