Proteopedia

2a0i

F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNAF Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA

Structural highlights

2a0i is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.72Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRAI1_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. Relaxosome formation requires binding of IHF and TraY to the oriT region, which then faciliates binding of TraI relaxase. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA. DNA transfer occurs via the conjugative pore (transferosome) an intercellular junction mediated by a type IV secretion system, with TraD providing the means to link the relaxosome to the conjugative pore. The relaxase completes DNA transfer by reversing the covalent phosphotyrosine linkage and releasing the T-strand.[1] [2] [3] [4] [5] TraI has also been identified as DNA helicase I. DNA. helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner.[6] [7] [8] [9] [10]

Evolutionary Conservation

 

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The TraI protein of conjugative plasmid F factor binds and cleaves a single-stranded region of the plasmid prior to transfer to a recipient. TraI36, an N-terminal TraI fragment, binds ssDNA with a subnanomolar K(D) and remarkable sequence specificity. The structure of the TraI36 Y16F variant bound to ssDNA reveals specificity determinants, including a ssDNA intramolecular 3 base interaction and two pockets within the protein's binding cleft that accommodate bases in a knob-into-hole fashion. Mutagenesis results underscore the intricate design of the binding site, with the greatest effects resulting from substitutions for residues that both contact ssDNA and stabilize protein structure. The active site architecture suggests that the bound divalent cation, which is essential for catalysis, both positions the DNA by liganding two oxygens of the scissile phosphate and increases the partial positive charge on the phosphorus to enhance nucleophilic attack.

Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase.,Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF Structure. 2005 Oct;13(10):1533-44. PMID:16216584[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
  2. ↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
  3. ↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
  4. ↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
  5. ↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
  6. ↑ Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF. Subdomain organization and catalytic residues of the F factor TraI relaxase domain. Biochim Biophys Acta. 2003 Mar 21;1646(1-2):86-99. PMID:12637015
  7. ↑ Abdel-Monem M, Taucher-Scholz G, Klinkert MQ. Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4659-63. PMID:6308637
  8. ↑ Matson SW, Nelson WC, Morton BS. Characterization of the reaction product of the oriT nicking reaction catalyzed by Escherichia coli DNA helicase I. J Bacteriol. 1993 May;175(9):2599-606. PMID:8386720
  9. ↑ Nelson WC, Howard MT, Sherman JA, Matson SW. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J Biol Chem. 1995 Nov 24;270(47):28374-80. PMID:7499339
  10. ↑ Stern JC, Schildbach JF. DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA. Biochemistry. 2001 Sep 25;40(38):11586-95. PMID:11560509
  11. ↑ Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF. Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase. Structure. 2005 Oct;13(10):1533-44. PMID:16216584 doi:10.1016/j.str.2005.06.013

2a0i, resolution 2.72Å

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