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


Other title
F plasmid
TraM family
Type of item
Degree grantor
University of Alberta
Author or creator
Peng, Yun
Supervisor and department
Glover, Mark
Examining committee member and department
Fahlman, Richard (Biochemistry)
Raivio, Tracy (Biological Sciences)
MacMillan, Andrew (Biochemistry)
Department of Biochemistry

Date accepted
Graduation date
Master of Science
Degree level
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 a pair of TraM tetramers cooperatively binds an underwound sbmA site that contains 12 base pairs/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 β-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 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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