3d8a - Revision history

OCA at 12:42, 30 August 2023

2023-08-30T12:42:35Z

← Older revision		Revision as of 12:42, 30 August 2023
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	<StructureSection load='3d8a' size='340' side='right'caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='3d8a' size='340' side='right'caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d8a]] is a 16 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=3D8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~2g7o~~\|~~2g7o~~]]~~</div>~~</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]] 2.55Å</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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [https://pdbe.org/3d8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [https://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [https://pdbe.org/3d8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [https://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Edwards~~, R A~~]]		[[Category: Edwards RA]]
	[[Category: Glover~~, J N.M~~]]		[[Category: Glover JNM]]
	[[Category: Lu, J]]		[[Category: Lu J]]
	[[Category: Wong~~, J J]]~~		[[Category: Wong JJ]]
	~~[[Category: Atp-binding]]~~
	~~[[Category: Conjugation]]~~
	~~[[Category: Dna binding protein]]~~
	~~[[Category: Dna-binding]]~~
	~~[[Category: Inner membrane]]~~
	~~[[Category: Membrane]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Protein complex]]~~
	~~[[Category: Trad c-terminal peptide]]~~
	~~[[Category: Tram tetramerization domain]]~~
	~~[[Category: Transmembrane~~]]

OCA at 07:56, 2 February 2022

2022-02-02T07:56:29Z

← Older revision		Revision as of 07:56, 2 February 2022
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	<StructureSection load='3d8a' size='340' side='right'caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='3d8a' size='340' side='right'caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g7o\|2g7o]]</div></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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [~~http~~://pdbe.org/3d8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [https://pdbe.org/3d8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [https://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:45, 7 August 2019

2019-08-07T06:45:38Z

← Older revision		Revision as of 06:45, 7 August 2019
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	==Co-crystal structure of TraM-TraD complex.==		==Co-crystal structure of TraM-TraD complex.==
	<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='3d8a' size='340' side='right'caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8a_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8a_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Edwards, R A]]		[[Category: Edwards, R A]]
	[[Category: Glover, J N.M]]		[[Category: Glover, J N.M]]

OCA at 08:31, 3 August 2017

2017-08-03T08:31:39Z

← Older revision		Revision as of 08:31, 3 August 2017
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	<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d8a]] is a 16 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=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</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]), traD, ECOK12F102 ([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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://pdbe.org/3d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://pdbe.org/3d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a 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> [[http://www.uniprot.org/uniprot/TRAD1_ECOLI TRAD1_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. Couples the transferosome to a type IV secretion system. Probably forms a pore through which single-stranded plasmid DNA is transferred to the secretion system. The last 37 residues are important for determining plasmid specificity and transfer efficiency, with additional specificity conferred by the TraD-TraM pair.<ref>PMID:9811665</ref>		[[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Ecoli]]~~
	[[Category: Edwards, R A]]		[[Category: Edwards, R A]]
	[[Category: Glover, J N.M]]		[[Category: Glover, J N.M]]

OCA at 08:12, 5 August 2016

2016-08-05T08:12:56Z

← Older revision		Revision as of 08:12, 5 August 2016
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	==Co-crystal structure of TraM-TraD complex.==		==Co-crystal structure of TraM-TraD complex.==
	<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure with sequence from [http://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=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[3d8a]] is a 16 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=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</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 ~~Escherichia coli K-12~~]), traD, ECOK12F102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</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]), traD, ECOK12F102 ([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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a 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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://pdbe.org/3d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d8a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d8a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3d8a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia coli k-12~~]]		[[Category: Ecoli]]
	[[Category: Edwards, R A]]		[[Category: Edwards, R A]]
	[[Category: Glover, J N.M]]		[[Category: Glover, J N.M]]

OCA at 17:10, 25 December 2014

2014-12-25T17:10:51Z

← Older revision		Revision as of 17:10, 25 December 2014
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	<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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a 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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a 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> [[http://www.uniprot.org/uniprot/TRAD1_ECOLI TRAD1_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. Couples the transferosome to a type IV secretion system. Probably forms a pore through which single-stranded plasmid DNA is transferred to the secretion system. The last 37 residues are important for determining plasmid specificity and transfer efficiency, with additional specificity conferred by the TraD-TraM pair.<ref>PMID:9811665</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:06, 12 November 2014

2014-11-12T08:06:49Z

← Older revision		Revision as of 08:06, 12 November 2014
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	[[Image:~~3d8a~~.~~png~~\|~~left~~\|~~200px~~]]		==Co-crystal structure of TraM-TraD complex.==
			<StructureSection load='3d8a' size='340' side='right' caption='[[3d8a]], [[Resolution\|resolution]] 2.55Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3d8a]] is a 16 chain structure with sequence from [http://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=3D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D8A FirstGlance]. <br>
			</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2g7o\|2g7o]]</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 Escherichia coli K-12]), traD, ECOK12F102 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d8a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d8a RCSB], [http://www.ebi.ac.uk/pdbsum/3d8a PDBsum]</span></td></tr>
			</table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/3d8a_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			F plasmid-mediated bacterial conjugation requires interactions between a relaxosome component, TraM, and the coupling protein TraD, a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. Here we present the crystal structure of the C-terminal tail of TraD bound to the TraM tetramerization domain, the first structural evidence of relaxosome-coupling protein interactions. The structure reveals the TraD C-terminal peptide bound to each of four symmetry-related grooves on the surface of the TraM tetramer. Extensive protein-protein interactions were observed between the two proteins. Mutational analysis indicates that these interactions are specific and required for efficient F conjugation in vivo. Our results suggest that specific interactions between the C-terminal tail of TraD and the TraM tetramerization domain might lead to more generalized interactions that stabilize the relaxosome-coupling protein complex in preparation for conjugative DNA transfer.

	~~{{STRUCTURE_3d8a\| PDB=3d8a \| SCENE= }}~~		Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation.,Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN Mol Microbiol. 2008 Oct;70(1):89-99. Epub 2008 Aug 19. PMID:18717787<ref>PMID:18717787</ref>

	~~===Co-crystal structure~~ of ~~TraM-TraD complex~~.~~===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18717787}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3d8a]] is a 16 chain structure with sequence from [http://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=3D8A OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018717787<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Edwards, R A.]]		[[Category: Edwards, R A]]
	[[Category: Glover, J N.M.]]		[[Category: Glover, J N.M]]
	[[Category: Lu, J.]]		[[Category: Lu, J]]
	[[Category: Wong, J J.]]		[[Category: Wong, J J]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Conjugation]]		[[Category: Conjugation]]

OCA: Protected "3d8a" [edit=sysop:move=sysop]

2013-01-07T20:43:20Z

Protected "3d8a" [edit=sysop:move=sysop]

← Older revision	Revision as of 20:43, 7 January 2013
(No difference)

OCA at 20:43, 7 January 2013

2013-01-07T20:43:16Z

← Older revision		Revision as of 20:43, 7 January 2013
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	~~{{Seed}}~~
	[[Image:3d8a.png\|left\|200px]]		[[Image:3d8a.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3d8a", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
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	{{STRUCTURE_3d8a\| PDB=3d8a \| SCENE= }}		{{STRUCTURE_3d8a\| PDB=3d8a \| SCENE= }}

	===Co-crystal structure of TraM-TraD complex.===		===Co-crystal structure of TraM-TraD complex.===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18717787}}, adds the Publication Abstract to the page~~
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	{{ABSTRACT_PUBMED_18717787}}		{{ABSTRACT_PUBMED_18717787}}

	==About this Structure==		==About this Structure==
	~~3D8A~~ is a 16 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA].		[[3d8a]] is a 16 chain structure with sequence from [http://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=3D8A OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18717787~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018717787</ref><references group="xtra"/>
	[[Category: Escherichia coli ~~k12~~]]		[[Category: Escherichia coli k-12]]
	[[Category: Edwards, R A.]]		[[Category: Edwards, R A.]]
	[[Category: Glover, J N.M.]]		[[Category: Glover, J N.M.]]
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	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Conjugation]]		[[Category: Conjugation]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna-binding]]		[[Category: Dna-binding]]
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	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	~~[[Category: Plasmid]]~~
	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: Trad c-terminal peptide]]		[[Category: Trad c-terminal peptide]]
	[[Category: Tram tetramerization domain]]		[[Category: Tram tetramerization domain]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:43:53 2009''~~

OCA at 21:44, 17 February 2009

2009-02-17T21:44:00Z

← Older revision		Revision as of 21:44, 17 February 2009
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	==About this Structure==		==About this Structure==
	3D8A is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA].		3D8A is a 16 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D8A OCA].

	==Reference==		==Reference==
	~~Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation., Lu J, Wong JJ, Edwards RA, Manchak J, Frost LS, Glover JN, Mol Microbiol. 2008 Aug 19.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18717787 18717787]~~		<ref group="xtra">PMID:18717787</ref><references group="xtra"/>
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
	~~[[Category: Protein complex]]~~
	[[Category: Edwards, R A.]]		[[Category: Edwards, R A.]]
	[[Category: Glover, J N.M.]]		[[Category: Glover, J N.M.]]
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	[[Category: Transmembrane]]		[[Category: Transmembrane]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Oct 15 12~~:46:~~33 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:43:53 2009''