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4qpo

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==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==
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<StructureSection load='4qpo' size='340' side='right' caption='[[4qpo]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='4qpo' size='340' side='right'caption='[[4qpo]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.999&#8491;</td></tr>
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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=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>
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<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>
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<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>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[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>
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Edwards, R A]]
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[[Category: Escherichia coli K-12]]
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[[Category: Frost, L S]]
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[[Category: Large Structures]]
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[[Category: Glover, J N.M]]
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[[Category: Edwards RA]]
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[[Category: Lu, J]]
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[[Category: Frost LS]]
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[[Category: Peng, Y]]
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[[Category: Glover JNM]]
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[[Category: Wong, J]]
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[[Category: Lu J]]
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[[Category: Dna binding]]
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[[Category: Peng Y]]
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[[Category: Rhh domain]]
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[[Category: Wong J]]
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[[Category: Transcription]]
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Current revision

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

PDB ID 4qpo

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