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Korasick DA, Campbell AC, Christgen SL, Chakravarthy S, White TA, Becker DF, Tanner JJ. Redox Modulation of Oligomeric State in Proline Utilization A. Biophys J 2019; 114:2833-2843. [PMID: 29925020 DOI: 10.1016/j.bpj.2018.04.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 10/28/2022] Open
Abstract
Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique among PutAs in that it forms a tetramer in solution. Curiously, a dimeric BjPutA hot spot mutant was previously shown to display wild-type catalytic activity despite lacking the tetrameric structure. These observations raised the question of what is the active oligomeric state of BjPutA. Herein, we investigate the factors that contribute to tetramerization of BjPutA in vitro. Negative-stain electron microscopy indicates that BjPutA is primarily dimeric at nanomolar concentrations, suggesting concentration-dependent tetramerization. Further, sedimentation-velocity analysis of BjPutA at high (micromolar) concentration reveals that although the binding of active-site ligands does not alter oligomeric state, reduction of the flavin adenine dinucleotide cofactor results in dimeric protein. Size-exclusion chromatography coupled with multiangle light scattering and small-angle x-ray scattering analysis also reveals that reduced BjPutA is dimeric. Taken together, these results suggest that the BjPutA oligomeric state is dependent upon both enzyme concentration and the redox state of the flavin cofactor. This is the first report, to our knowledge, of redox-linked oligomerization in the PutA family.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Shelbi L Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois
| | - Tommi A White
- Department of Biochemistry, University of Missouri, Columbia, Missouri; Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri; Department of Chemistry, University of Missouri, Columbia, Missouri.
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2
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Christgen SL, Zhu W, Sanyal N, Bibi B, Tanner JJ, Becker DF. Discovery of the Membrane Binding Domain in Trifunctional Proline Utilization A. Biochemistry 2017; 56:6292-6303. [PMID: 29090935 PMCID: PMC6044449 DOI: 10.1021/acs.biochem.7b01008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli proline utilization A (EcPutA) is the archetype of trifunctional PutA flavoproteins, which function both as regulators of the proline utilization operon and bifunctional enzymes that catalyze the four-electron oxidation of proline to glutamate. EcPutA shifts from a self-regulating transcriptional repressor to a bifunctional enzyme in a process known as functional switching. The flavin redox state dictates the function of EcPutA. Upon proline oxidation, the flavin becomes reduced, triggering a conformational change that causes EcPutA to dissociate from the put regulon and bind to the cellular membrane. Major structure/function domains of EcPutA have been characterized, including the DNA-binding domain, proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase catalytic domains, and an aldehyde dehydrogenase superfamily fold domain. Still lacking is an understanding of the membrane-binding domain, which is essential for EcPutA catalytic turnover and functional switching. Here, we provide evidence for a conserved C-terminal motif (CCM) in EcPutA having a critical role in membrane binding. Deletion of the CCM or replacement of hydrophobic residues with negatively charged residues within the CCM impairs EcPutA functional and physical membrane association. Furthermore, cell-based transcription assays and limited proteolysis indicate that the CCM is essential for functional switching. Using fluorescence resonance energy transfer involving dansyl-labeled liposomes, residues in the α-domain are also implicated in membrane binding. Taken together, these experiments suggest that the CCM and α-domain converge to form a membrane-binding interface near the PRODH domain. The discovery of the membrane-binding region will assist efforts to define flavin redox signaling pathways responsible for EcPutA functional switching.
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Affiliation(s)
- Shelbi L. Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Weidong Zhu
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Nikhilesh Sanyal
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Bushra Bibi
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Liu LK, Becker DF, Tanner JJ. Structure, function, and mechanism of proline utilization A (PutA). Arch Biochem Biophys 2017; 632:142-157. [PMID: 28712849 DOI: 10.1016/j.abb.2017.07.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/13/2023]
Abstract
Proline has important roles in multiple biological processes such as cellular bioenergetics, cell growth, oxidative and osmotic stress response, protein folding and stability, and redox signaling. The proline catabolic pathway, which forms glutamate, enables organisms to utilize proline as a carbon, nitrogen, and energy source. FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent glutamate semialdehyde dehydrogenase (GSALDH) convert proline to glutamate in two sequential oxidative steps. Depletion of PRODH and GSALDH in humans leads to hyperprolinemia, which is associated with mental disorders such as schizophrenia. Also, some pathogens require proline catabolism for virulence. A unique aspect of proline catabolism is the multifunctional proline utilization A (PutA) enzyme found in Gram-negative bacteria. PutA is a large (>1000 residues) bifunctional enzyme that combines PRODH and GSALDH activities into one polypeptide chain. In addition, some PutAs function as a DNA-binding transcriptional repressor of proline utilization genes. This review describes several attributes of PutA that make it a remarkable flavoenzyme: (1) diversity of oligomeric state and quaternary structure; (2) substrate channeling and enzyme hysteresis; (3) DNA-binding activity and transcriptional repressor function; and (4) flavin redox dependent changes in subcellular location and function in response to proline (functional switching).
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Affiliation(s)
- Li-Kai Liu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, United States.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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Moxley MA, Zhang L, Christgen S, Tanner JJ, Becker DF. Identification of a Conserved Histidine As Being Critical for the Catalytic Mechanism and Functional Switching of the Multifunctional Proline Utilization A Protein. Biochemistry 2017; 56:3078-3088. [PMID: 28558236 DOI: 10.1021/acs.biochem.7b00046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Proline utilization A from Escherichia coli (EcPutA) is a multifunctional flavoenzyme that oxidizes proline to glutamate through proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH) activities, while also switching roles as a DNA-bound transcriptional repressor and a membrane-bound catabolic enzyme. This phenomenon, termed functional switching, occurs through a redox-mediated mechanism in which flavin reduction triggers a conformational change that increases EcPutA membrane binding affinity. Structural studies have shown that reduction of the FAD cofactor causes the ribityl moiety to undergo a crankshaft motion, indicating that the orientation of the ribityl chain is a key element of PutA functional switching. Here, we test the role of a conserved histidine that bridges from the FAD pyrophosphate to the backbone amide of a conserved leucine residue in the PRODH active site. An EcPutA mutant (H487A) was characterized by steady-state and rapid-reaction kinetics, and cell-based reporter gene experiments. The catalytic activity of H487A is severely diminished (>50-fold) with membrane vesicles as the electron acceptor, and H487A exhibits impaired lipid binding and in vivo transcriptional repressor activity. Rapid-reaction kinetic experiments demonstrate that H487A is 3-fold slower than wild-type EcPutA in a conformational change step following reduction of the FAD cofactor. Furthermore, the reduction potential (Em) of H487A is ∼40 mV more positive than that of wild-type EcPutA, and H487A has an attenuated ability to catalyze the reverse PRODH chemical step of reoxidation by P5C. In this process, significant red semiquinone forms in contrast to the same reaction with wild-type EcPutA, in which facile two-electron reoxidation occurs without the formation of a measurable amount of semiquinone. These results indicate that His487 is critically important for the proline/P5C chemical step, conformational change kinetics, and functional switching in EcPutA.
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Affiliation(s)
- Michael A Moxley
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Lu Zhang
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Shelbi Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
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Arentson BW, Hayes EL, Zhu W, Singh H, Tanner JJ, Becker DF. Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA. Biosci Rep 2016; 36:e00413. [PMID: 27742866 PMCID: PMC5293562 DOI: 10.1042/bsr20160435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/05/2016] [Accepted: 10/14/2016] [Indexed: 01/18/2023] Open
Abstract
Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon-helix-helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the bifunctional Rhodobacter capsulatus PutA (RcPutA) in order to explore the modular design of functional switching in trifunctional PutAs. The EcRHH-RcPutA chimaera retains the catalytic properties of RcPutA while acquiring the oligomeric state, quaternary structure and DNA-binding properties of EcPutA. Furthermore, the EcRHH-RcPutA chimaera exhibits proline-induced lipid association, which is a fundamental characteristic of functional switching. Unexpectedly, RcPutA lipid binding is also activated by proline, which shows for the first time that bifunctional PutAs exhibit a limited form of functional switching. Altogether, these results suggest that the C-terminal domain (CTD), which is conserved by trifunctional PutAs and certain bifunctional PutAs, is essential for functional switching in trifunctional PutAs.
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Affiliation(s)
- Benjamin W Arentson
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Erin L Hayes
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Weidong Zhu
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, U.S.A
- Protein Technologies and Assays, Research and Development, MilliporeSigma, 2909 Laclede Avenue, St. Louis, MO 63103, U.S.A
| | - John J Tanner
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, U.S.A
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, U.S.A
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A.
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Luo M, Christgen S, Sanyal N, Arentson BW, Becker DF, Tanner JJ. Evidence that the C-terminal domain of a type B PutA protein contributes to aldehyde dehydrogenase activity and substrate channeling. Biochemistry 2014; 53:5661-73. [PMID: 25137435 PMCID: PMC4159212 DOI: 10.1021/bi500693a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
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Proline utilization A (PutA) is a
bifunctional enzyme that catalyzes
the oxidation of proline to glutamate. Structures of type A PutAs
have revealed the catalytic core consisting of proline dehydrogenase
(PRODH) and Δ1-pyrroline-5-carboxylate dehydrogenase
(P5CDH) modules connected by a substrate-channeling tunnel. Type B
PutAs also have a C-terminal domain of unknown function (CTDUF) that
is absent in type A PutAs. Small-angle X-ray scattering (SAXS), mutagenesis,
and kinetics are used to determine the contributions of this domain
to PutA structure and function. The 1127-residue Rhodobacter
capsulatus PutA (RcPutA) is used as a representative CTDUF-containing
type B PutA. The reaction progress curve for the coupled PRODH–P5CDH
activity of RcPutA does not exhibit a time lag, implying a substrate
channeling mechanism. RcPutA is monomeric in solution, which is unprecedented
for PutAs. SAXS rigid body modeling with target–decoy validation
is used to build a model of RcPutA. On the basis of homology to aldehyde
dehydrogenases (ALDHs), the CTDUF is predicted to consist of a β-hairpin
fused to a noncatalytic Rossmann fold domain. The predicted tertiary
structural interactions of the CTDUF resemble the quaternary structural
interactions in the type A PutA dimer interface. The model is tested
by mutagenesis of the dimerization hairpin of a type A PutA and the
CTDUF hairpin of RcPutA. Similar functional phenotypes are observed
in the two sets of variants, supporting the hypothesis that the CTDUF
mimics the type A PutA dimer interface. These results suggest annotation
of the CTDUF as an ALDH superfamily domain that facilitates P5CDH
activity and substrate channeling by stabilizing the aldehyde-binding
site and sealing the substrate-channeling tunnel from the bulk medium.
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Affiliation(s)
- Min Luo
- Department of Chemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States
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Anbazhagan V, Sankhala RS, Singh BP, Swamy MJ. Isothermal titration calorimetric studies on the interaction of the major bovine seminal plasma protein, PDC-109 with phospholipid membranes. PLoS One 2011; 6:e25993. [PMID: 22022488 PMCID: PMC3193528 DOI: 10.1371/journal.pone.0025993] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 09/15/2011] [Indexed: 11/19/2022] Open
Abstract
The interaction of the major bovine seminal plasma protein, PDC-109 with lipid membranes was investigated by isothermal titration calorimetry. Binding of the protein to model membranes made up of diacyl phospholipids was found to be endothermic, with positive values of binding enthalpy and entropy, and could be analyzed in terms of a single type of binding sites on the protein. Enthalpies and entropies for binding to diacylphosphatidylcholine membranes increased with increase in temperature, although a clear-cut linear dependence was not observed. The entropically driven binding process indicates that hydrophobic interactions play a major role in the overall binding process. Binding of PDC-109 with dimyristoylphosphatidylcholine membranes containing 25 mol% cholesterol showed an initial increase in the association constant as well as enthalpy and entropy of binding with increase in temperature, whereas the values decreased with further increase in temperature. The affinity of PDC-109 for phosphatidylcholine increased at higher pH, which is physiologically relevant in view of the basic nature of the seminal plasma. Binding of PDC-109 to Lyso-PC could be best analysed in terms of two types of binding interactions, a high affinity interaction with Lyso-PC micelles and a low-affinity interaction with the monomeric lipid. Enthalpy-entropy compensation was observed for the interaction of PDC-109 with phospholipid membranes, suggesting that water structure plays an important role in the binding process.
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Affiliation(s)
- V. Anbazhagan
- School of Chemistry, University of Hyderabad, Hyderabad, Andhra Pradesh, India
| | | | - Bhanu Pratap Singh
- School of Chemistry, University of Hyderabad, Hyderabad, Andhra Pradesh, India
| | - Musti J. Swamy
- School of Chemistry, University of Hyderabad, Hyderabad, Andhra Pradesh, India
- * E-mail:
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhang W, Zhang M, Zhu W, Zhou Y, Wanduragala S, Rewinkel D, Tanner JJ, Becker DF. Redox-induced changes in flavin structure and roles of flavin N(5) and the ribityl 2'-OH group in regulating PutA--membrane binding. Biochemistry 2007; 46:483-91. [PMID: 17209558 PMCID: PMC2527739 DOI: 10.1021/bi061935g] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PutA is a novel flavoprotein in Escherichia coli that switches from a transcriptional repressor to a membrane-bound proline catabolic enzyme. Previous crystallographic studies of the PutA proline dehydrogenase (PRODH) domain under oxidizing conditions revealed that FAD N(5) and the ribityl 2'-OH group form hydrogen bonds with Arg431 and Arg556, respectively. Here we identify molecular interactions in the PutA PRODH active site that underlie redox-dependent functional switching of PutA. We report that reduction of the PRODH domain induces major structural changes in the FAD cofactor, including a 22 degrees bend of the isoalloxazine ring along the N(5)-N(10) axis, crankshaft rotation of the upper part of the ribityl chain, and formation of a new hydrogen bond network involving the ribityl 2'-OH group, FAD N(1), and Gly435. The roles of the FAD 2'-OH group and the FAD N(5)-Arg431 hydrogen bond pair in regulating redox-dependent PutA-membrane associations were tested using FAD analogues and site-directed mutagenesis. Kinetic membrane binding measurements and cell-based reporter gene assays of modified PutA proteins show that disrupting the FAD N(5)-Arg431 interaction impairs the reductive activation of PutA-membrane binding. We also show that the FAD 2'-OH group acts as a redox-sensitive toggle switch that controls PutA-membrane binding. These results illustrate a new versatility of the ribityl chain in flavoprotein mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | - Donald F. Becker
- Address Correspondence to: Donald F. Becker, Phone: 402-472-9652; Fax: 402-472-472-7842. E-mail:
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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