Article thumbnail

Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM

By Joyce J. W. Wong, Jun Lu, Ross A. Edwards, Laura S. Frost and J. N. Mark Glover


The conjugative transfer of F-like plasmids such as F, R1, R100 and pED208, between bacterial cells requires TraM, a plasmid-encoded DNA-binding protein. TraM tetramers bridge the origin of transfer (oriT) to a key component of the conjugative pore, the coupling protein TraD. Here we show that TraM recognizes a high-affinity DNA-binding site, sbmA, as a cooperative dimer of tetramers. The crystal structure of the TraM–sbmA complex from the plasmid pED208 shows that binding cooperativity is mediated by DNA kinking and unwinding, without any direct contact between tetramers. Sequence-specific DNA recognition is carried out by TraM’s N-terminal ribbon–helix–helix (RHH) domains, which bind DNA in a staggered arrangement. We demonstrate that both DNA-binding specificity, as well as selective interactions between TraM and the C-terminal tail of its cognate TraD mediate conjugation specificity within the F-like family of plasmids. The ability of TraM to cooperatively bind DNA without interaction between tetramers leaves the C-terminal TraM tetramerization domains free to make multiple interactions with TraD, driving recruitment of the plasmid to the conjugative pore

Topics: Structural Biology
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (2008). 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
  2. (2010). A stevedore’s protein knot.
  3. (2009). Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.
  4. (2001). Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
  5. (2008). An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage.
  6. (2002). Analysis and characterization of the IncFV plasmid pED208 transfer region.
  7. (1994). Analysis of the sequence and gene products of the transfer region of the F sex factor.
  8. (2008). ARP/wARP and molecular replacement: The next generation. Acta Crystallogr.
  9. (2008). Bacterial actin: Architecture of the ParMRC plasmid DNA partitioning complex.
  10. (2007). Bacterial pathogenomics.
  11. (2009). Biological diversity of prokaryotic type IV secretion systems.
  12. (1983). Characterization of conjugative plasmid EDP208.
  13. (1991). Characterization of the oriT region of the IncFV plasmid pED208.
  14. (2002). Characterizing the DNA contacts and cooperative binding of F plasmid TraM to its cognate sites at oriT.
  15. (2003). Conjugative coupling proteins interact with cognate and heterologous VirB10-like proteins while exhibiting specificity for cognate relaxosomes.
  16. (2010). Conjugative DNA metabolism in gram-negative bacteria.
  17. (2004). Coot: Model-building tools for molecular graphics.
  18. (1999). Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain.
  19. (2004). Crystal structure of an IdeR-DNA complex reveals a conformational change in activated IdeR for base-specific interactions.
  20. (1996). Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn.
  21. (2008). Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in staphylococcus epidermidis.
  22. (1999). Crystal structure of the iron-dependent regulator (IdeR) from mycobacterium tuberculosis shows both metal binding sites fully occupied.
  23. (2008). Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding.
  24. (2010). Crystal structure of TtgV in complex with its DNA operator reveals a general model for cooperative DNA binding of tetrameric gene regulators.
  25. (2010). Crystal structures of the multidrug binding repressor corynebacteriumglutamicum CgmR in complex with inducers and with an operator.
  26. (1998). Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr.
  27. (1991). Deletion analysis of the F plasmid oriT locus.
  28. (2008). Dissemination of clonally related escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15.
  29. (2004). DNA binding properties of protein TrwA, a possible structural variant of the arc repressor superfamily.
  30. (1995). DNA processing reactions in bacterial conjugation.
  31. (1962). Episomic element in a strain of salmonella typhosa.
  32. (2003). Evidence for a monomeric intermediate in the reversible unfolding
  33. (2003). Extent of single-stranded DNA required for efficient TraI helicase activity in vitro.
  34. (2003). F factor conjugation is a true type IV secretion system.
  35. (2001). F plasmid conjugative DNA transfer: the TraI helicase activity is essential for DNA strand transfer.
  36. (1963). Infective heredity of multiple drug resistance in bacteria.
  37. (2000). Mobilization of chimeric oriT plasmids by F and R100-1: Role of relaxosome formation in defining plasmid specificity.
  38. (2010). Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases.
  39. (2004). Mutational analysis of TraM correlates oligomerization and DNA binding with autoregulation and conjugative DNA transfer.
  40. (2005). Mutations in the C-terminal region of TraM provide evidence for in vivo TraM-TraD interactions during F-plasmid conjugation.
  41. (1997). Nicking by transesterification: The reaction catalysed by a relaxase.
  42. (2009). Plasmid-mediated quinolone resistance: a multifaceted threat.
  43. (1984). Processing of plasmid DNA during bacterial conjugation.
  44. (1997). Processing of X-ray diffraction data collected in oscillation mode.
  45. (2006). Protonation-mediated structural flexibility in the F conjugation regulatory protein,
  46. (1997). Refinement of macromolecular structures by the maximum-likelihood method.
  47. (1996). Regulation of the expression of the traM gene of the F sex factor of escherichia coli.
  48. (2007). Ribbon-helix-helix transcription factors: Variations on a theme.
  49. (2007). Segrosome structure revealed by a complex of ParR with centromere DNA.
  50. (1953). Sex in bacteria; genetic studies,
  51. (2010). Single-stranded DNA binding by F TraI relaxase and helicase domains are coordinately regulated.
  52. (1994). Site- and strand-specific nicking at oriT of plasmid R100 in a purified system: Enhancement of the nicking activity of TraI (helicase I) with TraY and IHF.
  53. (2001). Solution structure of the DNA-binding domain of TraM.
  54. (1991). Specific DNA binding of the TraM protein to the oriT region of plasmid R100.
  55. (1995). Stepwise assembly of a relaxosome at the F plasmid origin of transfer.
  56. (2002). Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.
  57. (2008). Structural basis of specific TraD-TraM recognition during F plasmid-mediated bacterial conjugation.
  58. (2003). Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
  59. (1998). Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex.
  60. (2002). Structure-function analysis of escherichia coli DNA helicase I reveals non-overlapping transesterase and helicase domains.
  61. (1995). Studies on the binding of integration host factor (IHF) and TraM to the origin of transfer of the IncFV plasmid pED208.
  62. (2007). The ATPase activity of the DNA transporter TrwB is modulated by protein TrwA: Implications for a common assembly mechanism of DNA translocating motors.
  63. (1998). The carboxyl terminus of protein TraD adds specificity and efficiency to F-plasmid conjugative transfer.
  64. (1997). The cytoplasmic DNA-binding protein TraM binds to the inner membrane protein TraD in vitro.
  65. (1999). The essential transfer protein TraM binds to DNA as a tetramer.
  66. (2007). The F plasmid-encoded TraM protein stimulates relaxosome-mediated cleavage at oriT through an interaction with TraI.
  67. (1998). The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
  68. (1991). The TraM protein of plasmid R1 is a DNA-binding protein.
  69. (1992). The TraM protein of the conjugative plasmid F binds to the origin of transfer of the F and ColE1 plasmids.
  70. (1995). The traY gene product and integration host factor stimulate escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT.
  71. (2004). Thirty-eight C-terminal amino acids of the coupling protein TraD of the F-like conjugative resistance plasmid R1 are required and sufficient to confer binding to the substrate selector protein TraM.
  72. (1989). Three-dimensional crystal structures of escherichia coli met repressor with and without corepressor.
  73. (1993). TraM of plasmid R1 regulates its own expression.
  74. (1998). Transfer protein TraM stimulates TraI-catalyzed cleavage of the transfer origin of plasmid R1 in vivo.
  75. (2001). Transfer protein TraY of plasmid R1 stimulates TraI-catalyzed oriT cleavage in vivo.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.