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2A0I

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

Summary for 2A0I
Entry DOI10.2210/pdb2a0i/pdb
Related1P4D
DescriptorF plasmid single-stranded oriT DNA, TraI protein, MAGNESIUM ION, ... (5 entities in total)
Functional Keywordssingle-stranded dna, protein-dna complex, 5-strand antiparallel beta sheet, hydrolase-dna complex, hydrolase/dna
Biological sourceEscherichia coli
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Cellular locationCytoplasm : P14565
Total number of polymer chains2
Total formula weight43352.37
Authors
Larkin, C.,Datta, S.,Harley, M.J.,Anderson, B.J.,Ebie, A.,Hargreaves, V.,Schildbach, J.F. (deposition date: 2005-06-16, release date: 2005-10-25, Last modification date: 2023-08-23)
Primary citationLarkin, C.,Datta, S.,Harley, M.J.,Anderson, B.J.,Ebie, A.,Hargreaves, V.,Schildbach, J.F.
Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase.
Structure, 13:1533-1544, 2005
Cited by
PubMed Abstract: 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.
PubMed: 16216584
DOI: 10.1016/j.str.2005.06.013
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.72 Å)
Structure validation

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