Identifikation und funktionelle Charakterisierung von TrpD2, einer neuen Klasse nukleinsäurebindender Proteine

Daniel Schneider
2013
Determining the functions of uncharacterized proteins is one of the most challenging tasks of the post genomic era. Today, the TrEMBL database contains over 16 million entries and their number is still growing almost exponentially. Conservative estimations assume that at least one third of these sequences have unknown, uncertain or incorrectly annotated functions. This fact emphasizes the importance of functional analysis to enhance our knowledge of the protein function space. Although
more » ... . Although promising computational approaches for functional assignment have already been developed, biochemical analyses are still indispensable to definitely determine the physiological role of such proteins. Functional annotation can greatly be facilitated by including initial knowledge, such as an evolutionary relationship of unknown proteins with well characterized homologous enzymes. Those protein pairs have presumably evolved from a common ancestor by gene duplication and diversification. One example for such proteins with unknown function is the TrpD2 family. These proteins are closely related to the anthranilate phosphoribosyltransferase (TrpD), a homodimeric enzyme involved in tryptophan biosynthesis. Additionally, TrpD2 shows a more divergent relationship to the nucleoside phosphorylases class II (NP-II) that have a role in the nucleotide salvage pathway. The TrpD2 group consists of about 140 proteins that occur widespread among Bacteria, but not in Archaea. They share on average 17 percent sequence identity with TrpD and about 10 percent with NP-II proteins, but catalyze neither the TrpD nor the NP-II reaction. Within this work the function of the TrpD2 protein family was analyzed with methods of computational biology, structural biology, biochemistry, microbiology and genetics. Most experiments were carried out with the TrpD2 protein from E. coli, YbiB. As a first step the crystal structure of YbiB was solved in collaboration with the group of Olga Mayans. It is overall very similar to the structure of TrpD (r.m.s.d. = 2.4 Å for [...]
doi:10.5283/epub.23060 fatcat:lhseion6dvdd3ohuizrxdzrxvy