1P4D

F factor TraI Relaxase Domain

Summary for 1P4D

• Entry DOI: 10.2210/pdb1p4d/pdb
• Descriptor: TraI protein, MAGNESIUM ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: 5-strand antiparallel beta sheet, alpha-beta, 3 histidine mg(ii) coordination, hydrolase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : P14565
• Total number of polymer chains: 3
• Total formula weight: 109783.30

Authors

Datta, S.,Larkin, C.,Schildbach, J.F. (deposition date: 2003-04-22, release date: 2003-10-14, Last modification date: 2024-02-14)

Primary citation

Datta, S.,Larkin, C.,Schildbach, J.F.
Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
Structure, 11:1369-1379, 2003

PubMed 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.

PubMed: 14604527
DOI: 10.1016/j.str.2003.10.001

Experimental method

X-RAY DIFFRACTION (2.6 Å)