Integration host factor (IHF) is a small heterodimeric protein that binds the minor groove of DNA in a sequence-specific manner and induces a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription . The core structure of IHF consists of a partly opened 4-helical bundle that is capped with a beta-sheet.
Prokaryotic protein HU and the bacteriophage SPO1 transcription factor TF1 are closely related to IHF. These proteins are collectively referred to as type II DNA-binding proteins (DBPII), forming a group of basic, dimeric proteins found in all bacteria that are able to bind DNA to induce and stabilise DNA bending. HU plays a structural role in replication initiation, transcription regulation, site-specific recombination, and the compaction of the bacterial genome . TF1 is essential for viral multiplication .
The DNA-binding domain of the TraM protein , an essential component of the DNA transfer machinery of the conjugative resistance plasmid R1, appears to have a similar structure to DBPII .