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Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein

Nature Structural Biology volume 10, pages 109–114 (2003)Cite this article

Abstract

The PutA flavoprotein from Escherichia coli plays multiple roles in proline catabolism by functioning as a membrane-associated bi-functional enzyme and a transcriptional repressor of proline utilization genes. The human homolog of the PutA proline dehydrogenase (PRODH) domain is critical in p53-mediated apoptosis and schizophrenia. Here we report the crystal structure of a 669-residue truncated form of PutA that shows both PRODH and DNA-binding activities, representing the first structure of a PutA protein and a PRODH enzyme from any organism. The structure is a domain-swapped dimer with each subunit comprising three domains: a helical dimerization arm, a 120-residue domain containing a three-helix bundle similar to that in the helix-turn-helix superfamily of DNA-binding proteins and a β/α-barrel PRODH domain with a bound lactate inhibitor. Analysis of the structure provides insight into the mechanism of proline oxidation to pyrroline-5-carboxylate, and functional studies of a mutant protein suggest that the DNA-binding domain is located within the N-terminal 261 residues of E. coli PutA.

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Figure 1: Reactions catalyzed by the 1,320-residue E. coli PutA protein.
Figure 2: Overall structure of PutA669.
Figure 3: The active site of PutA669.
Figure 4: The DNA-binding function of PutA669.

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Acknowledgements

This research was supported by grants from the NIH (J.J.T. and D.F.B) and the NSF (D.F.B.). We thank L. Beamer for collecting the NaBr derivative data, L. Beamer and P. Tipton for helpful comments on the manuscript, and the beamline personnel at APS SBC19-ID, NSLS X8C and NSLS X12B for technical assistance.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Missouri-Columbia, Columbia, 65211, Missouri, USA

    Yong-Hwan Lee, Shorena Nadaraia & John J. Tanner

  2. Department of Structural Biology Core, University of Missouri-Columbia, Columbia, 65211, Missouri, USA

    Yong-Hwan Lee

  3. Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, 63121, Missouri, USA

    Dan Gu & Donald F. Becker

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  1. Yong-Hwan Lee
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Correspondence to John J. Tanner.

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Lee, YH., Nadaraia, S., Gu, D. et al. Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein. Nat Struct Mol Biol 10, 109–114 (2003). https://doi.org/10.1038/nsb885

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