Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon of Escherichia coli

  • Functional profile of E. coli permease RutG
  • Maria Botou, Panayiota Lazou, Konstantinos Papakostas, George Lambrinidis, Thomas Evangelidis, Emmanuel Mikros, Stathis Frillingos
  • Molecular Microbiology, February 2018, Wiley
  • DOI: 10.1111/mmi.13931

Elucidation of specificity of bacterial uracil permeases

What is it about?

Bacteria use pyrimidine/purine transporters to control the intracellular levels of nucleotides and acquire external nitrogen sources for metabolism. We analyze for the first time the function and specificity of a major group of bacterial pyrimidine transporters and show that a single amino-acid change can cause a major shift in their substrate specificity preferences.

Why is it important?

It is well accepted that the prediction of substrate specificity of transporters based on sequence homology is difficult because of the flexibility of these membrane proteins for recognition of different substrates. On the other hand, transporters are one of the least well studied classes of proteins and experimental annotation is missing for the majority of microbial genes predicted to be transporters in the databases. In this work, we focus on one understudied group of bacterial homologs (the UraA cluster) in the nucleobase transporter family NAT/NCS2. We analyze the functional profiles of four homologs and highlight the role of a binding-site Phe residue in distinguishing uracil from thymine as a substrate in this class of homologs. Our analysis shows that, although the relation of sequence with substrate specificity is complex, the specificity deviations of these closely related transporters can be traced down to single amino acid changes.

Perspectives

Stathis Frillingos
University of Ioannina

A combined approach using phylogenetics, homology modeling, detailed functional profile analysis and carefully designed site-directed mutagenesis in four rationally selected homologs helped us elucidate a major determinant of specificity in the group of bacterial pyrimidine permeases studied here. I believe that this is a good paradigm of how systematic research can shed light on the specificity determinants of large homology groups of transporters that remain functionally understudied to date. We still have a lot to learn from these types of studies.

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http://dx.doi.org/10.1111/mmi.13931

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