Bioinformatic analysis of the TonB protein family
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TonB is a protein prevalent in a large number of Gram-negative bacteria that is believed to be responsible for the energy transduction component in the import of ferric iron complexes and vitamin B12 across the outer membrane. We have analyzed all the TonB proteins that are currently contained in the Entrez database and have identified nine different clusters based on its conserved 90-residue C-terminal domain amino acid sequence. The vast majority of the proteins contained a single predicted cytoplasmic transmembrane domain; however, nine of the TonB proteins encompass a ∼90 amino acid N-terminal extension homologous to the MecR1 protein, which is composed of three additional predicted transmembrane helices. The periplasmic linker region, which is located between the N-terminal domain and the C-terminal domain, is extremely variable both in length (22–283 amino acids) and in proline content, indicating that a Pro-rich domain is not a required feature for all TonB proteins. The secondary structure of the C-terminal domain is found to be well preserved across all families, with the most variable region being between the second α-helix and the third β-strand of the antiparallel β-sheet. The fourth β-strand found in the solution structure of the Escherichia coli TonB C-terminal domain is not a well conserved feature in TonB proteins in most of the clusters. Interestingly, several of the TonB proteins contained two C-terminal domains in series. This analysis provides a framework for future structure-function studies of TonB, and it draws attention to the unusual features of several TonB proteins.
KeywordsGram-negative bacteria Iron transport TonB Multiple sequence alignment
Heteronuclear single quantum coherence
multiple sequence alignment
nuclear overhauser effect
outer membrane transporter
This work was supported by an operating grant from the Canadian Institutes for Health Research (CIHR) to H.J.V.. R.S.P. was supported by Studentship awards from the Alberta Heritage Foundation for Medical Research (AHFMR) and the National Science and Engineering Research Council (NSERC). HJV holds a Scientist award from AHFMR. The NMR equipment used was obtained through grants from the Canada Foundation for Innovation, the Alberta Science and Research Authority (ASRA) and AHFMR. Maintenance of the Bio-NMR centre is supported by CIHR and the University of Calgary.
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