1p4d
F factor TraI Relaxase Domain
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| , resolution 2.60Å | |||||||
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| Ligands: | and | ||||||
| Gene: | TRAI (Escherichia coli) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
OverviewOverview
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 StructureAbout this Structure
1P4D is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
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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