HU-alpha binds to the putative double-stranded DNA mimic HI1450 from Haemophilus influenzae

Recently, the solution structure of the hypothetical protein HI1450 from Haemophilus influenzae was solved as part of a structure-based effort to understand function. The distribution of its many negatively charged residues and weak structure and sequence homology to uracil DNA glycosylase inhibitor (Ugi) suggested that HI1450 may act as a double-stranded DNA (dsDNA) mimic. We present supporting evidence here and show that HI1450 interacts with the dsDNA-binding protein HU-alpha. The interaction between HI1450 and HU-alpha from H. influenzae is characterized using calorimetry and NMR spectroscopy. HU-alpha binds to HI1450 with a K(d) of 3.0 +/- 0.2 microM, which is similar in affinity to its interaction with dsDNA. Chemical shift perturbation data indicate that the beta1-strand of HI1450 and neighboring regions are most directly involved in interactions with HU-alpha. These results show that HI1450 and its structural homolog, Ugi, use similar parts of their structures to recognize DNA-binding proteins.