1p4d | pdb_00001p4d
F factor TraI Relaxase Domain
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Overview
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.
About this Structure
1P4D is a Single protein structure of sequence from Escherichia coli with MG and EDO as ligands. Full crystallographic information is available from OCA.
Reference
Structural insights into single-stranded DNA binding and cleavage by F factor TraI., Datta S, Larkin C, Schildbach JF, Structure. 2003 Nov;11(11):1369-79. PMID:14604527
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