5yk4 - Revision history

OCA at 08:32, 22 November 2023

OCA — Wed, 22 Nov 2023 08:32:19 GMT

←Older revision		Revision as of 08:32, 22 November 2023
Line 1:		Line 1:

	==Mismatch Repair Protein==		==Mismatch Repair Protein==
-	<StructureSection load='5yk4' size='340' side='right' caption='[[5yk4]], [[Resolution\|resolution]] 2.97Å' scene=''>	+	<StructureSection load='5yk4' size='340' side='right'caption='[[5yk4]], [[Resolution\|resolution]] 2.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yk4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Neig1 Neig1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YK4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yk4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae_FA_1090 Neisseria gonorrhoeae FA 1090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YK4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 2.97Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5x9w\|5x9w~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~mutS, NGO1930 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=242231 NEIG1])~~</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=5yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk4 OCA], [https://pdbe.org/5yk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yk4 RCSB], [https://www.ebi.ac.uk/pdbsum/5yk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk4 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=5yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk4 OCA], [~~http~~://pdbe.org/5yk4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yk4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yk4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MUTS_NEIG1 MUTS_NEIG1]] This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.	+	[https://www.uniprot.org/uniprot/MUTS_NEIG1 MUTS_NEIG1] This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5yk4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yk4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA mismatch repair protein 3D structures\|DNA mismatch repair protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Neig1~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nair, D T~~]]	+	[[Category: Neisseria gonorrhoeae FA 1090]]
-	[[Category: ~~Nirwal, S~~]]	+	[[Category: Nair DT]]
-	[[Category: ~~Atpase]]~~	+	[[Category: Nirwal S]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Mismatch sensor]]~~	+
-	~~[[Category: Mut~~]]	+

OCA at 07:37, 13 December 2017

OCA — Wed, 13 Dec 2017 07:37:45 GMT

←Older revision		Revision as of 07:37, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5yk4' size='340' side='right' caption='[[5yk4]], [[Resolution\|resolution]] 2.97Å' scene=''>		<StructureSection load='5yk4' size='340' side='right' caption='[[5yk4]], [[Resolution\|resolution]] 2.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YK4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yk4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neig1 Neig1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YK4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x9w\|5x9w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x9w\|5x9w]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutS, NGO1930 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242231 NEIG1])</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=5yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk4 OCA], [http://pdbe.org/5yk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk4 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=5yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk4 OCA], [http://pdbe.org/5yk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MUTS_NEIG1 MUTS_NEIG1]] This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.		[[http://www.uniprot.org/uniprot/MUTS_NEIG1 MUTS_NEIG1]] This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The DNA mismatch repair (MMR) pathway removes errors that appear during genome replication. MutS is the primary mismatch sensor and forms an asymmetric dimer that encircles DNA to bend it to scan for mismatches. The mechanism utilized to load DNA into the central tunnel was unknown and the origin of the force required to bend DNA was unclear. We show that, in absence of DNA, MutS forms a symmetric dimer wherein a gap exists between the monomers through which DNA can enter the central tunnel. The comparison with structures of MutS-DNA complexes suggests that the mismatch scanning monomer (Bm) will move by nearly 50 A to associate with the other monomer (Am). Consequently, the N-terminal domains of both monomers will press onto DNA to bend it. The proposed mechanism of toroid formation evinces that the force required to bend DNA arises primarily due to the movement of Bm and hence, the MutS dimer acts like a pair of pliers to bend DNA. We also shed light on the allosteric mechanism that influences the expulsion of adenosine triphosphate from Am on DNA binding. Overall, this study provides mechanistic insight regarding the primary event in MMR i.e. the assembly of the MutS-DNA complex.
		+
		+	Mechanism of formation of a toroid around DNA by the mismatch sensor protein.,Nirwal S, Kulkarni DS, Sharma A, Rao DN, Nair DT Nucleic Acids Res. 2017 Nov 22. pii: 4647669. doi: 10.1093/nar/gkx1149. PMID:29182773<ref>PMID:29182773</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yk4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Neig1]]
	[[Category: Nair, D T]]		[[Category: Nair, D T]]
	[[Category: Nirwal, S]]		[[Category: Nirwal, S]]

OCA: Protected "5yk4" [edit=sysop:move=sysop]

OCA — Wed, 22 Nov 2017 07:46:31 GMT

Protected "5yk4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:46, 22 November 2017

OCA: New page: ==Mismatch Repair Protein== == Structural highlights ==
OCA — Wed, 22 Nov 2017 07:46:30 GMT

New page: ==Mismatch Repair Protein== <StructureSection load='5yk4' size='340' side='right' caption='5yk4, resolution 2.97Å' scene=''> == Structural highlights == <table><t...

New page

==Mismatch Repair Protein==
<StructureSection load='5yk4' size='340' side='right' caption='[[5yk4]], [[Resolution|resolution]] 2.97Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5yk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YK4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x9w|5x9w]]</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=5yk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk4 OCA], [http://pdbe.org/5yk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk4 ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/MUTS_NEIG1 MUTS_NEIG1]] This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.
TOC
</StructureSection>
[[Category: Nair, D T]]
[[Category: Nirwal, S]]
[[Category: Atpase]]
[[Category: Dna binding protein]]
[[Category: Mismatch sensor]]
[[Category: Mut]]