6e8e - Revision history

OCA at 06:20, 11 October 2023

OCA — Wed, 11 Oct 2023 06:20:47 GMT

←Older revision		Revision as of 06:20, 11 October 2023
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	<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6E8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_coli_O139:H28_str._E24377A Escherichia coli O139:H28 str. E24377A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E8E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.25Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">mutL, EcE24377A_4728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [https://pdbe.org/6e8e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [https://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e 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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [~~http~~://pdbe.org/6e8e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.	+	[https://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.[https://www.uniprot.org/uniprot/MUTL_ECOLI MUTL_ECOLI] This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of the final effector complex. The ATPase activity of MutL is stimulated by DNA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6e8e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6e8e" 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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
		+	[[Category: Escherichia coli O139:H28 str. E24377A]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almawi~~, A W~~]]	+	[[Category: Almawi AW]]
-	[[Category: Guarne, A]]	+	[[Category: Guarne A]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dna binding protein~~]]	+

OCA at 06:26, 7 October 2020

OCA — Wed, 07 Oct 2020 06:26:55 GMT

←Older revision		Revision as of 06:26, 7 October 2020
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	<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6E8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6E8E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutL, EcE24377A_4728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutL, EcE24377A_4728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [http://pdbe.org/6e8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [http://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e 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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [http://pdbe.org/6e8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [http://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:29, 23 May 2019

OCA — Thu, 23 May 2019 07:29:59 GMT

←Older revision		Revision as of 07:29, 23 May 2019
Line 3:		Line 3:
	<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E8E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mutL, EcE24377A_4728 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [http://pdbe.org/6e8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [http://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e 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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [http://pdbe.org/6e8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [http://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Almawi, A W]]		[[Category: Almawi, A W]]

OCA at 08:46, 1 May 2019

OCA — Wed, 01 May 2019 08:46:04 GMT

←Older revision		Revision as of 08:46, 1 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6e8e is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the Escherichia coli sliding clamp-MutL complex.==
		+	<StructureSection load='6e8e' size='340' side='right'caption='[[6e8e]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6e8e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E8E FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</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=6e8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e8e OCA], [http://pdbe.org/6e8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e8e RCSB], [http://www.ebi.ac.uk/pdbsum/6e8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e8e ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO3B_ECOLI DPO3B_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The beta-clamp is a protein hub central to DNA replication and fork management. Proteins interacting with the beta-clamp harbor a conserved clamp-binding motif that is often found in extended regions. Therefore, clamp interactions have -almost exclusively- been studied using short peptides recapitulating the binding motif. This approach has revealed the molecular determinants that mediate the binding but cannot describe how proteins with clamp-binding motifs embedded in structured domains are recognized. The mismatch repair protein MutL has an internal clamp-binding motif, but its interaction with the beta-clamp has different roles depending on the organism. In Bacillus subtilis, the interaction stimulates the endonuclease activity of MutL and it is critical for DNA mismatch repair. Conversely, disrupting the interaction between Escherichia coli MutL and the beta-clamp only causes a mild mutator phenotype. Here, we determined the structures of the regulatory domains of E. coli and B. subtilis MutL bound to their respective beta-clamps. The structures reveal different binding modes consistent with the binding to the beta-clamp being a two-step process. Functional characterization indicates that, within the regulatory domain, only the clamp binding motif is required for the interaction between the two proteins. However, additional motifs beyond the regulatory domain may stabilize the interaction. We propose a model for the activation of the endonuclease activity of MutL in organisms lacking methyl-directed mismatch repair.

-	~~Authors~~:	+	Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific.,Almawi AW, Scotland MK, Randall JR, Liu L, Martin HK, Sacre L, Shen Y, Pillon MC, Simmons LA, Sutton MD, Guarne A Nucleic Acids Res. 2019 Mar 27. pii: 5420525. doi: 10.1093/nar/gkz115. PMID:30916336<ref>PMID:30916336</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6e8e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Almawi, A W]]
		+	[[Category: Guarne, A]]
		+	[[Category: Complex]]
		+	[[Category: Dna binding protein]]

OCA at 14:46, 15 August 2018

OCA — Wed, 15 Aug 2018 14:46:57 GMT

←Older revision		Revision as of 14:46, 15 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6e8e is ON HOLD	+	The entry 6e8e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6e8e" [edit=sysop:move=sysop]

OCA — Thu, 09 Aug 2018 19:53:49 GMT

Protected "6e8e" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:53, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6e8e is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Aug 2018 19:53:48 GMT

New page: '''Unreleased structure''' The entry 6e8e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6e8e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]