The overall goal of this study is to provide molecular and structural understanding for the redox based functional switching of a multifunctional enzyme involved in regulating and catalyzing proline metabolism. The two-step conversion of proline to glutamate in Gram-negative bacteria is catalyzed by PutA (proline utilization A), a large membrane-associated flavoenzyme. PutA catalyzes the four-electron oxidation of proline to glutamate by coordinating the activities of separate flavin-dependent proline dehydrogenase (PRODH) and NAD+-dependent 1-pyrroline- 5-carboxylate dehydrogenase (P5CDH) domains. In certain prokaryotes such as Escherichia coli, PutA also contains a ribbon-helix-helix (RHH) DNA-binding domain and is an autogenous transcriptional repressor of the proline utilization genes putA and putP (encodes a high affinity proline transporter). To fulfill its mutually exclusiv functions as a transcriptional repressor and membrane-bound enzyme, PutA undergoes proline-dependent functional switching. Thus, PutAs with DNA binding activity are unique trifunctional flavoproteins that act as sensors of cellular metabolism by responding to proline availability. Earlier studies have established that proline reduction of the flavin activates PutA membrane- binding thereby triggering PutA switching from a transcriptional repressor to a membrane-bound enzyme. The principal hypothesis of this proposal is that redox signals in the flavin active site control the conformation, subcellular localization, and function of PutA. The goal of this study is to further examine this hypothesis by building a structural and dynamic model for how reduction of the flavin cofactor drives PutA functional switching. Several major milestones achieved in the previous funding period form the basis for the proposed studies. In particular, conformational changes in the flavin itself and surrounding active site residues were identified and shown to be critical for initiating functional switching. The thermodynamic and structural basis of the PutA repressor function was elucidated. The first crystal structure of a full-length bifunctional PutA was determined. The solution structure of a trifunctional PutA was modeled using SAXS data and crystal structures of domains. And most recently, the elusive membrane-binding domain of PutA was identified. These results provide an outstanding framework for understanding, at unprecedented detail, the molecular mechanisms whereby PutA transforms from a gene regulatory protein to a membrane-bound enzyme. A new direction integrated into this study is to understand how proline catabolism is coupled to reduction of the respiratory chain in vivo.
The specific aims are the following: 1. Determine the organization and structure of trifunctional PutA. 2. Characterize the bioenergetics of proline metabolism. 3. Elucidate the mechanism of functional switching in PutA.

Public Health Relevance

The amino acid proline has multifaceted roles that impact human health. Inborn errors in proline metabolic genes are manifested in neurological dysfunctions such as schizophrenia, increased incidence of seizures, connective tissue diseases, premature aging, and osteopenia. This project will further the understanding of proline metabolism in cancer preventing mechanisms, type I hyperprolinemia, schizophrenia susceptibility, and pathogens that rely on proline as a major fuel source, such as the causative agents of peptic ulcers (Helicobacter pylori) and African sleeping sickness (Trypanosoma brucei).

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM061068-10A1
Application #
8372629
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Anderson, Vernon
Project Start
2000-01-01
Project End
2016-05-31
Budget Start
2012-08-01
Budget End
2013-05-31
Support Year
10
Fiscal Year
2012
Total Cost
$308,375
Indirect Cost
$53,375
Name
University of Nebraska Lincoln
Department
Biochemistry
Type
Schools of Earth Sciences/Natur
DUNS #
555456995
City
Lincoln
State
NE
Country
United States
Zip Code
68588
Spencer, Andrea L M; Bagai, Ireena; Becker, Donald F et al. (2014) Protein/protein interactions in the mammalian heme degradation pathway: heme oxygenase-2, cytochrome P450 reductase, and biliverdin reductase. J Biol Chem 289:29836-58
Singh, Harkewal; Arentson, Benjamin W; Becker, Donald F et al. (2014) Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc Natl Acad Sci U S A 111:3389-94
Luo, Min; Christgen, Shelbi; Sanyal, Nikhilesh et al. (2014) Evidence that the C-terminal domain of a type B PutA protein contributes to aldehyde dehydrogenase activity and substrate channeling. Biochemistry 53:5661-73
Zhu, Weidong; Haile, Ashley M; Singh, Ranjan K et al. (2013) Involvement of the *3-*3 loop of the proline dehydrogenase domain in allosteric regulation of membrane association of proline utilization A. Biochemistry 52:4482-91
Moxley, Michael A; Becker, Donald F (2012) Rapid reaction kinetics of proline dehydrogenase in the multifunctional proline utilization A protein. Biochemistry 51:511-20
Singh, Ranjan K; Tanner, John J (2012) Unique structural features and sequence motifs of proline utilization A (PutA). Front Biosci (Landmark Ed) 17:556-68
Singh, Ranjan K; Larson, John D; Zhu, Weidong et al. (2011) Small-angle X-ray scattering studies of the oligomeric state and quaternary structure of the trifunctional proline utilization A (PutA) flavoprotein from Escherichia coli. J Biol Chem 286:43144-53
Becker, Donald F; Zhu, Weidong; Moxley, Michael A (2011) Flavin redox switching of protein functions. Antioxid Redox Signal 14:1079-91
Moxley, Michael A; Tanner, John J; Becker, Donald F (2011) Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli. Arch Biochem Biophys 516:113-20
Srivastava, Dhiraj; Schuermann, Jonathan P; White, Tommi A et al. (2010) Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum. Proc Natl Acad Sci U S A 107:2878-83

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