Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities

A methodology is proposed to solve a difficult modeling problem related to the recently sequenced P39 protein. This sequence shares no similarity with any known 3D structure, but a fold is proposed by several threading tools, The difficulty in aligning the target sequence on one of the proposed temp late structures is overcome by combining the results of several available p rediction methods and by refining a rational consensus between them, lit si lico validation of the obtained model and a preliminary crosscheck with exp erimental features allow us to state that this borderline prediction is at least reasonable. This model raises relevant hypotheses on the main structu ral features of the protein and allows the design of site-directed mutation s. Knowing the genetic context of the P39 reading frame, we are now able to suggest a function for the P39 protein: it would act as a periplasmic subs trate-binding protein.