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| | <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 == |
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| | __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]]
| + | |
| Structural highlights
Function
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.[1] [2] [3] [4]
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Di Laurenzio L, Frost LS, Paranchych W. The TraM protein of the conjugative plasmid F binds to the origin of transfer of the F and ColE1 plasmids. Mol Microbiol. 1992 Oct;6(20):2951-9. PMID:1479887
- ↑ Penfold SS, Simon J, Frost LS. Regulation of the expression of the traM gene of the F sex factor of Escherichia coli. Mol Microbiol. 1996 May;20(3):549-58. PMID:8736534
- ↑ Fekete RA, Frost LS. Characterizing the DNA contacts and cooperative binding of F plasmid TraM to its cognate sites at oriT. J Biol Chem. 2002 May 10;277(19):16705-11. Epub 2002 Mar 1. PMID:11875064 doi:http://dx.doi.org/10.1074/jbc.M111682200
- ↑ Ragonese H, Haisch D, Villareal E, Choi JH, Matson SW. The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI. Mol Microbiol. 2007 Feb;63(4):1173-84. PMID:17238924 doi:http://dx.doi.org/10.1111/j.1365-2958.2006.05576.x
- ↑ Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark Glover JN. Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM. J Mol Biol. 2014 Oct 2. pii: S0022-2836(14)00517-8. doi:, 10.1016/j.jmb.2014.09.018. PMID:25284757 doi:http://dx.doi.org/10.1016/j.jmb.2014.09.018
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