4qpo - Revision history

OCA at 12:47, 1 March 2024

OCA — Fri, 01 Mar 2024 12:47:51 GMT

←Older revision		Revision as of 12:47, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.999Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [https://pdbe.org/4qpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [https://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [https://pdbe.org/4qpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [https://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_ECOLI] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>		[https://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_ECOLI] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon-helix-helix) domain bound to its sbmA site. The structure indicates that a pair of TraM tetramers cooperatively binds an underwound sbmA site containing 12 base pairs per turn. The sbmA is composed of 4 copies of a 5-base-pair motif, each of which is recognized by an RHH domain. The structure reveals that a single conservative amino acid difference in the RHH beta-ribbon between F and pED208 TraM changes its specificity for its cognate 5-base-pair sequence motif. Specificity is also dictated by the positioning of 2-base-pair spacer elements within sbmA; in F sbmA, the spacers are positioned between motifs 1 and 2 and between motifs 3 and 4, whereas in pED208 sbmA, there is a single spacer between motifs 2 and 3. We also demonstrate that a pair of F TraM tetramers can cooperatively bind its sbmC site with an affinity similar to that of sbmA in spite of a lack of sequence similarity between these DNA elements. These results provide a basis for the prediction of the DNA binding properties of the family of TraM proteins.
-
-	Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM.,Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark Glover JN J Mol Biol. 2014 Oct 2. pii: S0022-2836(14)00517-8. doi:, 10.1016/j.jmb.2014.09.018. PMID:25284757<ref>PMID:25284757</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4qpo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:45, 22 February 2023

OCA — Wed, 22 Feb 2023 13:45:44 GMT

←Older revision		Revision as of 13:45, 22 February 2023
Line 3:		Line 3:
	<StructureSection load='4qpo' size='340' side='right'caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qpo' size='340' side='right'caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qpo]] is a 4 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=4QPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">traM, ECOK12F071 ([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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [https://pdbe.org/4qpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [https://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [~~http~~://pdbe.org/4qpo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_ECOLI]] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>	+	[https://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_ECOLI] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Edwards~~, R A~~]]	+	[[Category: Edwards RA]]
-	[[Category: Frost~~, L S~~]]	+	[[Category: Frost LS]]
-	[[Category: Glover~~, J N.M~~]]	+	[[Category: Glover JNM]]
-	[[Category: Lu, J]]	+	[[Category: Lu J]]
-	[[Category: Peng, Y]]	+	[[Category: Peng Y]]
-	[[Category: Wong, J]]	+	[[Category: Wong J]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Rhh domain]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 09:44, 24 April 2019

OCA — Wed, 24 Apr 2019 09:44:48 GMT

←Older revision		Revision as of 09:44, 24 April 2019
Line 1:		Line 1:

	==Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM==		==Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM==
-	<StructureSection load='4qpo' size='340' side='right' caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4qpo' size='340' side='right'caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qpo]] is a 4 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=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">traM, ECOK12F071 ([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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://pdbe.org/4qpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://pdbe.org/4qpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Edwards, R A]]		[[Category: Edwards, R A]]
	[[Category: Frost, L S]]		[[Category: Frost, L S]]

OCA at 18:59, 4 August 2016

OCA — Thu, 04 Aug 2016 18:59:03 GMT

←Older revision		Revision as of 18:59, 4 August 2016
Line 1:		Line 1:
		+
	==Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM==		==Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM==
	<StructureSection load='4qpo' size='340' side='right' caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qpo' size='340' side='right' caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://pdbe.org/4qpo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qpo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4qpo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:11, 25 December 2014

OCA — Thu, 25 Dec 2014 12:11:29 GMT

←Older revision		Revision as of 12:11, 25 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TRAM1_ECOLI TRAM1_ECOLI]] Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair.<ref>PMID:1479887</ref> <ref>PMID:8736534</ref> <ref>PMID:11875064</ref> <ref>PMID:17238924</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:29, 17 December 2014

OCA — Wed, 17 Dec 2014 10:29:29 GMT

←Older revision		Revision as of 10:29, 17 December 2014
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Edwards, R A.]]	+	[[Category: Edwards, R A]]
-	[[Category: Frost, L S.]]	+	[[Category: Frost, L S]]
-	[[Category: Glover, J N.M.]]	+	[[Category: Glover, J N.M]]
-	[[Category: Lu, J.]]	+	[[Category: Lu, J]]
-	[[Category: Peng, Y.]]	+	[[Category: Peng, Y]]
-	[[Category: Wong, J.]]	+	[[Category: Wong, J]]
	[[Category: Dna binding]]		[[Category: Dna binding]]
	[[Category: Rhh domain]]		[[Category: Rhh domain]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 08:53, 22 October 2014

OCA — Wed, 22 Oct 2014 08:53:41 GMT

←Older revision		Revision as of 08:53, 22 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo 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=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The conjugative transfer of bacterial F plasmids relies on TraM, a plasmid-encoded protein that recognizes multiple DNA sites to recruit the plasmid to the conjugative pore. In spite of the high degree of amino acid sequence conservation between TraM proteins, many of these proteins have markedly different DNA binding specificities that ensure the selective recruitment of a plasmid to its cognate pore. Here we present the structure of F TraM RHH (ribbon-helix-helix) domain bound to its sbmA site. The structure indicates that a pair of TraM tetramers cooperatively binds an underwound sbmA site containing 12 base pairs per turn. The sbmA is composed of 4 copies of a 5-base-pair motif, each of which is recognized by an RHH domain. The structure reveals that a single conservative amino acid difference in the RHH beta-ribbon between F and pED208 TraM changes its specificity for its cognate 5-base-pair sequence motif. Specificity is also dictated by the positioning of 2-base-pair spacer elements within sbmA; in F sbmA, the spacers are positioned between motifs 1 and 2 and between motifs 3 and 4, whereas in pED208 sbmA, there is a single spacer between motifs 2 and 3. We also demonstrate that a pair of F TraM tetramers can cooperatively bind its sbmC site with an affinity similar to that of sbmA in spite of a lack of sequence similarity between these DNA elements. These results provide a basis for the prediction of the DNA binding properties of the family of TraM proteins.
		+
		+	Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM.,Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark Glover JN J Mol Biol. 2014 Oct 2. pii: S0022-2836(14)00517-8. doi:, 10.1016/j.jmb.2014.09.018. PMID:25284757<ref>PMID:25284757</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:14, 4 September 2014

OCA — Thu, 04 Sep 2014 06:14:27 GMT

←Older revision		Revision as of 06:14, 4 September 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM==
-		+	<StructureSection load='4qpo' size='340' side='right' caption='[[4qpo]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~The entry~~ 4qpo is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qpo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QPO FirstGlance]. <br>
-	~~Authors~~: ~~Peng, Y~~., ~~Lu, J~~., ~~Wong, J~~., Edwards, R.A., Frost, L.S., Glover, J.N.M.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
-		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qpo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qpo RCSB], [http://www.ebi.ac.uk/pdbsum/4qpo PDBsum]</span></td></tr>
-	~~Description~~: ~~Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein~~, ~~TraM~~	+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Edwards, R A.]]
		+	[[Category: Frost, L S.]]
		+	[[Category: Glover, J N.M.]]
		+	[[Category: Lu, J.]]
		+	[[Category: Peng, Y.]]
		+	[[Category: Wong, J.]]
		+	[[Category: Dna binding]]
		+	[[Category: Rhh domain]]
		+	[[Category: Transcription]]

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

OCA — Wed, 02 Jul 2014 07:27:59 GMT

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

←Older revision

Revision as of 07:27, 2 July 2014

OCA: New page: '''Unreleased structure''' The entry 4qpo is ON HOLD Authors: Peng, Y., Lu, J., Wong, J., Edwards, R.A., Frost, L.S., Glover, J.N.M. Description: Mechanistic basis of plasmid-specific ...

OCA — Wed, 02 Jul 2014 07:27:57 GMT

New page: '''Unreleased structure''' The entry 4qpo is ON HOLD Authors: Peng, Y., Lu, J., Wong, J., Edwards, R.A., Frost, L.S., Glover, J.N.M. Description: Mechanistic basis of plasmid-specific ...

New page

'''Unreleased structure'''

The entry 4qpo is ON HOLD

Authors: Peng, Y., Lu, J., Wong, J., Edwards, R.A., Frost, L.S., Glover, J.N.M.

Description: Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM