[Frontiers in Bioscience 17, 556-568, January 1, 2012]

Unique structural features and sequence motifs of proline utilization A (PutA)

Ranjan K. Singh1, John J. Tanner1

1Departments of Chemistry and Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Comparison of a bifunctional PutA with monofunctional PRODH and P5CDH
3.1. Structure of a minimalist PutA
3.2. The PutA PRODH barrel has an extra helix involved in FAD binding and substrate channeling
3.3. An extra helix at the C-terminus of PutA plugs the substrate-channeling cavity
3.4. BjPutA has domains not found in the monofunctional enzymes
4. The conserved C-terminal motif of branch 1 PutAs
5. Beyond the minimalist PutA
5.1. The DNA-binding domain of trifunctional PutA
5.2. The C-terminal domain of unknown function
6. Summary
7. Acknowledgements
8. References

1. ABSTRACT

Proline utilization A proteins (PutAs) are bifunctional enzymes that catalyze the oxidation of proline to glutamate using spatially separated proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase active sites. Here we use the crystal structure of the minimalist PutA from Bradyrhizobium japonicum (BjPutA) along with sequence analysis to identify unique structural features of PutAs. This analysis shows that PutAs have secondary structural elements and domains not found in the related monofunctional enzymes. Some of these extra features are predicted to be important for substrate channeling in BjPutA. Multiple sequence alignment analysis shows that some PutAs have a 17-residue conserved motif in the C-terminal 20-30 residues of the polypeptide chain. The BjPutA structure shows that this motif helps seal the internal substrate-channeling cavity from the bulk medium. Finally, it is shown that some PutAs have a 100-200 residue domain of unknown function in the C-terminus that is not found in minimalist PutAs. Remote homology detection suggests that this domain is homologous to the oligomerization beta-hairpin and Rossmann fold domain of BjPutA.