Structural insights into single-stranded DNA binding and cleavage by F factor TraI

Structure. 2003 Nov;11(11):1369-79. doi: 10.1016/j.str.2003.10.001.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA Helicases / chemistry*
  • DNA Helicases / physiology*
  • DNA, Single-Stranded / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Electrons
  • Endonucleases / metabolism
  • Escherichia coli Proteins
  • F Factor / chemistry*
  • Histidine / chemistry
  • Kinetics
  • Magnesium / chemistry
  • Magnesium / metabolism
  • Models, Molecular
  • Phosphates / chemistry
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Replication Origin
  • Software
  • Tyrosine / chemistry

Substances

  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Phosphates
  • Tyrosine
  • Histidine
  • DNA
  • Endonucleases
  • TraI protein, E coli
  • DNA Helicases
  • Magnesium

Associated data

  • PDB/1P4D