title: Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
abstract: Conjugative plasmid transfer between bacteria disseminates antibiotic resistance and diversifies prokaryotic genomes. Relaxases, proteins essential for conjugation, cleave one plasmid strand sequence specifically prior to transfer. Cleavage occurs through a Mg(2+)-dependent transesterification involving a tyrosyl hydroxyl and a DNA phosphate. The structure of the F plasmid TraI relaxase domain, described here, is a five-strand beta sheet flanked by alpha helices. The protein resembles replication initiator protein AAV-5 Rep but is circularly permuted, yielding a different topology. The beta sheet forms a binding cleft lined with neutral, nonaromatic residues, unlike most single-stranded DNA binding proteins which use aromatic and charged residues. The cleft contains depressions, suggesting base recognition occurs in a knob-into-hole fashion. Unlike most nucleases, three histidines but no acidic residues coordinate a Mg(2+) located near the catalytic tyrosine. The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage.
authors: Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
authors: Saumen
authors: S
authors: Datta
authors: Chris
authors: C
authors: Larkin
authors: Joel F
authors: JF
authors: Schildbach
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D004265:DNA Helicases / Q000737:chemistry* / Q000502:physiology*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004583:Electrons; D004720:Endonucleases / Q000378:metabolism; D029968:Escherichia coli Proteins; D005144:F Factor / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D010710:Phosphates / Q000737:chemistry; D010957:Plasmids / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D018741:Replication Origin; D012984:Software; D014443:Tyrosine / Q000737:chemistry
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D010710:Phosphates; D014443:Tyrosine; D006639:Histidine; D004247:DNA; D004720:Endonucleases; C027093:TraI protein, E coli; D004265:DNA Helicases; D008274:Magnesium