1
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Zhang X, Ouyang Z. Crystal structure of aldehyde dehydrogenase 1A1 from mouse. Biochem Biophys Res Commun 2022; 628:141-146. [DOI: 10.1016/j.bbrc.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
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2
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Buckley DP, Migaud ME, Tanner JJ. Conformational Preferences of Pyridone Adenine Dinucleotides from Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:11866. [PMID: 36233167 PMCID: PMC9570408 DOI: 10.3390/ijms231911866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022] Open
Abstract
Pyridone adenine dinucleotides (ox-NADs) are redox inactive derivatives of the enzyme cofactor and substrate nicotinamide adenine dinucleotide (NAD) that have a carbonyl group at the C2, C4, or C6 positions of the nicotinamide ring. These aberrant cofactor analogs accumulate in cells under stress and are potential inhibitors of enzymes that use NAD(H). We studied the conformational landscape of ox-NADs in solution using molecular dynamics simulations. Compared to NAD+ and NADH, 2-ox-NAD and 4-ox-NAD have an enhanced propensity for adopting the anti conformation of the pyridone ribose group, whereas 6-ox-NAD exhibits greater syn potential. Consequently, 2-ox-NAD and 4-ox-NAD have increased preference for folding into compact conformations, whereas 6-ox-NAD is more extended. ox-NADs have distinctive preferences for the orientation of the pyridone amide group, which are driven by intramolecular hydrogen bonding and steric interactions. These conformational preferences are compared to those of protein-bound NAD(H). Our results may help in identifying enzymes targeted by ox-NADs.
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Affiliation(s)
- David P. Buckley
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Marie E. Migaud
- Mitchell Cancer Institute, Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
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3
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Ye P, Li X, Cui B, Song S, Shen F, Chen X, Wang G, Zhou X, Deng Y. Proline utilization A controls bacterial pathogenicity by sensing its substrate and cofactors. Commun Biol 2022; 5:496. [PMID: 35614320 PMCID: PMC9132996 DOI: 10.1038/s42003-022-03451-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Previous reports indicate that proline utilization A (PutA) is involved in the oxidation of proline to glutamate in many bacteria. We demonstrate here that in addition to its role in proline catabolism, PutA acts as a global regulator to control the important biological functions and virulence of Ralstonia solanacearum. PutA regulates target gene expression levels by directly binding to promoter DNA, and its regulatory activity is enhanced by L-proline. Intriguingly, we reveal that the cofactors NAD+ and FAD boost the enzymatic activity of PutA for converting L-proline to L-glutamic acid but inhibit the regulatory activity of PutA for controlling target gene expression. Our results present evidence that PutA is a proline metabolic enzyme that also functions as a global transcriptional regulator in response to its substrate and cofactors and provide insights into the complicated regulatory mechanism of PutA in bacterial physiology and pathogenicity.
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Affiliation(s)
- Peiyi Ye
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xia Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Shihao Song
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Fangfang Shen
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xiayu Chen
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Gerun Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xiaofan Zhou
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.
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4
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Bogner AN, Ji J, Tanner JJ. Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel 2022; 35:gzac016. [PMID: 36448708 PMCID: PMC9801229 DOI: 10.1093/protein/gzac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its importance in cancer cell metabolism. Because human PRODH is challenging to purify, the PRODH domains of the bacterial bifunctional enzyme proline utilization A (PutA) have been used for inhibitor development. These systems have limitations due to large polypeptide chain length, conformational flexibility and the presence of domains unrelated to PRODH activity. Herein, we report the engineering of minimal PRODH domains for inhibitor discovery. The best designs contain one-third of the 1233-residue PutA from Sinorhizobium meliloti and include a linker that replaces the PutA α-domain. The minimal PRODHs exhibit near wild-type enzymatic activity and are susceptible to known inhibitors and inactivators. Crystal structures of minimal PRODHs inhibited by S-(-)-tetrahydro-2-furoic acid and 2-(furan-2-yl)acetic acid were determined at 1.23 and 1.72 Å resolution. Minimal PRODHs should be useful in chemical probe discovery.
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Affiliation(s)
- Alexandra N Bogner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
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5
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Mao Y, Seravalli J, Smith TG, Morton M, Tanner JJ, Becker DF. Evidence for Proline Catabolic Enzymes in the Metabolism of Thiazolidine Carboxylates. Biochemistry 2021; 60:3610-3620. [PMID: 34752700 DOI: 10.1021/acs.biochem.1c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiazolidine carboxylates such as thiazolidine-4-carboxylate (T4C) and thiazolidine-2-carboxylate (T2C) are naturally occurring sulfur analogues of proline. These compounds have been observed to have both beneficial and toxic effects in cells. Given that proline dehydrogenase has been proposed to be a key enzyme in the oxidative metabolism of thioprolines, we characterized T4C and T2C as substrates of proline catabolic enzymes using proline utilization A (PutA), which is a bifunctional enzyme with proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) activities. PutA is shown here to catalyze the FAD-dependent PRODH oxidation of both T4C and T2C with catalytic efficiencies significantly higher than with proline. Stopped-flow experiments also demonstrate that l-T4C and l-T2C reduce PutA-bound FAD at rates faster than proline. Unlike proline, however, oxidation of T4C and T2C does not generate a substrate for NAD+-dependent GSALDH. Instead, PutA/PRODH oxidation of T4C leads to cysteine formation, whereas oxidation of T2C generates an apparently stable Δ4-thiazoline-2-carboxylate species. Our results provide new insights into the metabolism of T2C and T4C.
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Affiliation(s)
- Yizi Mao
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Javier Seravalli
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Thomas G Smith
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Martha Morton
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
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6
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Campbell AC, Prater AR, Bogner AN, Quinn TP, Gates KS, Becker DF, Tanner JJ. Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles. ACS Chem Biol 2021; 16:2268-2279. [PMID: 34542291 DOI: 10.1021/acschembio.1c00427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Proline dehydrogenase (PRODH) is a flavoenzyme that catalyzes the first step of proline catabolism, the oxidation of l-proline to Δ1-pyrroline-5-carboxylate. PRODH has emerged as a cancer therapy target because of its involvement in the metabolic reprogramming of cancer cells. Here, we report the discovery of a new class of PRODH inactivator, which covalently and irreversibly modifies the FAD in a light-dependent manner. Two examples, 1,3-dithiolane-2-carboxylate and tetrahydrothiophene-2-carboxylate, have been characterized using X-ray crystallography (1.52-1.85 Å resolution), absorbance spectroscopy, and enzyme kinetics. The structures reveal that in the dark, these compounds function as classical reversible, proline analogue inhibitors. However, exposure of enzyme-inhibitor cocrystals to bright white light induces decarboxylation of the inhibitor and covalent attachment of the residual S-heterocycle to the FAD N5 atom, locking the cofactor into a reduced, inactive state. Spectroscopic measurements of the inactivation process in solution confirm the requirement for light and show that blue light is preferred. Enzyme activity assays show that the rate of inactivation is enhanced by light and that the inactivation is irreversible. We also demonstrate the photosensitivity of cancer cells to one of these compounds. A possible mechanism is proposed involving photoexcitation of the FAD, while the inhibitor is noncovalently bound in the active site, followed by electron transfer, decarboxylation, and radical combination steps. Our results could lead to the development of photopharmacological drugs targeting PRODH.
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Affiliation(s)
- Ashley C. Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Austin R. Prater
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Thomas P. Quinn
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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7
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Korasick DA, Christgen SL, Qureshi IA, Becker DF, Tanner JJ. Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). Arch Biochem Biophys 2021; 712:109025. [PMID: 34506758 DOI: 10.1016/j.abb.2021.109025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022]
Abstract
In many bacteria, the reactions of proline catabolism are catalyzed by the bifunctional enzyme known as proline utilization A (PutA). PutA catalyzes the two-step oxidation of l-proline to l-glutamate using distinct proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) active sites, which are separated by over 40 Å and connected by a complex tunnel system. The tunnel system consists of a main tunnel that connects the two active sites and functions in substrate channeling, plus six ancillary tunnels whose functions are unknown. Here we used tunnel-blocking mutagenesis to probe the role of a dynamic ancillary tunnel (tunnel 2a) whose shape is modulated by ligand binding to the PRODH active site. The 1.90 Å resolution crystal structure of Geobacter sulfurreducens PutA variant A206W verified that the side chain of Trp206 cleanly blocks tunnel 2a without perturbing the surrounding structure. Steady-state kinetic measurements indicate the mutation impaired PRODH activity without affecting the GSALDH activity. Single-turnover experiments corroborated a severe impairment of PRODH activity with flavin reduction decreased by nearly 600-fold in A206W relative to wild-type. Substrate channeling is also significantly impacted as A206W exhibited a 3000-fold lower catalytic efficiency in coupled PRODH-GSALDH activity assays, which measure NADH formation as a function of proline. The structure suggests that Trp206 inhibits binding of the substrate l-proline by preventing the formation of a conserved glutamate-arginine ion pair and closure of the PRODH active site. Our data are consistent with tunnel 2a serving as an open space through which the glutamate of the ion pair travels during the opening and closing of the active site in response to binding l-proline. These results confirm the essentiality of the conserved ion pair in binding l-proline and support the hypothesis that the ion pair functions as a gate that controls access to the PRODH active site.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Shelbi L Christgen
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Insaf A Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Donald F Becker
- Department Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, 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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8
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Campbell AC, Bogner AN, Mao Y, Becker DF, Tanner JJ. Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-γ-semialdehyde dehydrogenase active site of bifunctional proline utilization A. Arch Biochem Biophys 2020; 698:108727. [PMID: 33333077 DOI: 10.1016/j.abb.2020.108727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 01/31/2023]
Abstract
Proline utilization A (PutA) proteins are bifunctional proline catabolic enzymes that catalyze the 4-electron oxidation of l-proline to l-glutamate using spatially-separated proline dehydrogenase and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH, a.k.a. ALDH4A1) active sites. The observation that l-proline inhibits both the GSALDH activity of PutA and monofunctional GSALDHs motivated us to study the inhibition of PutA by proline stereoisomers and analogs. Here we report five high-resolution crystal structures of PutA with the following ligands bound in the GSALDH active site: d-proline, trans-4-hydroxy-d-proline, cis-4-hydroxy-d-proline, l-proline, and trans-4-hydroxy-l-proline. Three of the structures are of ternary complexes of the enzyme with an inhibitor and either NAD+ or NADH. To our knowledge, the NADH complex is the first for any GSALDH. The structures reveal a conserved mode of recognition of the inhibitor carboxylate, which results in the pyrrolidine rings of the d- and l-isomers having different orientations and different hydrogen bonding environments. Activity assays show that the compounds are weak inhibitors with millimolar inhibition constants. Curiously, although the inhibitors occupy the aldehyde binding site, kinetic measurements show the inhibition is uncompetitive. Uncompetitive inhibition may involve proline binding to a remote site or to the enzyme-NADH complex. Together, the structural and kinetic data expand our understanding of how proline-like molecules interact with GSALDH, reveal insight into the relationship between stereochemistry and inhibitor affinity, and demonstrate the pitfalls of inferring the mechanism of inhibition from crystal structures alone.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Alexandra N Bogner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Yizi Mao
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, 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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9
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Campbell AC, Robinson R, Mena-Aguilar D, Sobrado P, Tanner JJ. Structural Determinants of Flavin Dynamics in a Class B Monooxygenase. Biochemistry 2020; 59:4609-4616. [PMID: 33226785 DOI: 10.1021/acs.biochem.0c00783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ornithine hydroxylase known as SidA is a class B flavin monooxygenase that catalyzes the first step in the biosynthesis of hydroxamate-containing siderophores in Aspergillus fumigatus. Crystallographic studies of SidA revealed that the FAD undergoes dramatic conformational changes between out and in states during the catalytic cycle. We sought insight into the origins and purpose of flavin motion in class B monooxygenases by probing the function of Met101, a residue that contacts the pyrimidine ring of the in FAD. Steady-state kinetic measurements showed that the mutant variant M101A has a 25-fold lower turnover number. Pre-steady-state kinetic measurements, pH profiles, and solvent kinetic isotope effect measurements were used to isolate the microscopic step that is responsible for the reduced steady-state activity. The data are consistent with a bottleneck in the final step of the mechanism, which involves flavin dehydration and the release of hydroxy-l-ornithine and NADP+. Crystal structures were determined for M101A in the resting state and complexed with NADP+. The resting enzyme structure is similar to that of wild-type SidA, consistent with M101A exhibiting normal kinetics for flavin reduction by NADPH and wild-type affinity for NADPH. In contrast, the structure of the M101A-NADP+ complex unexpectedly shows the FAD adopting the out conformation and may represent a stalled conformation that is responsible for the slow kinetics. Altogether, our data support a previous proposal that one purpose of the FAD conformational change from in to out in class B flavin monooxygenases is to eject spent NADP+ in preparation for a new catalytic cycle.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Reeder Robinson
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Didier Mena-Aguilar
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States.,Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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10
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Hou J, Adhikari B, Tanner JJ, Cheng J. SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data. Proteins 2020; 88:775-787. [PMID: 31860156 PMCID: PMC7230021 DOI: 10.1002/prot.25865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/18/2019] [Accepted: 12/14/2019] [Indexed: 12/27/2022]
Abstract
Many proteins are composed of several domains that pack together into a complex tertiary structure. Multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for individual domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the orientations between domains. Small-angle X-ray scattering (SAXS) reports the structural properties of entire proteins and has the potential for guiding homology modeling of multidomain proteins. In this article, we describe a novel multidomain protein assembly modeling method, SAXSDom that integrates experimental knowledge from SAXS with probabilistic Input-Output Hidden Markov model to assemble the structures of individual domains together. Four SAXS-based scoring functions were developed and tested, and the method was evaluated on multidomain proteins from two public datasets. Incorporation of SAXS information improved the accuracy of domain assembly for 40 out of 46 critical assessment of protein structure prediction multidomain protein targets and 45 out of 73 multidomain protein targets from the ab initio domain assembly dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at https://github.com/jianlin-cheng/SAXSDom.
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Affiliation(s)
- Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA
| | - Badri Adhikari
- Department of Computer Science, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
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11
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Campbell AC, Becker DF, Gates KS, Tanner JJ. Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate. ACS Chem Biol 2020; 15:936-944. [PMID: 32159324 DOI: 10.1021/acschembio.9b00935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the FAD-dependent 2-electron oxidation of l-proline to Δ1-pyrroline-5-carboxylate. PRODH has emerged as a possible cancer therapy target, and thus the inhibition of PRODH is of interest. Here we show that the proline analogue thiazolidine-2-carboxylate (T2C) is a mechanism-based inactivator of PRODH. Structures of the bifunctional proline catabolic enzyme proline utilization A (PutA) determined from crystals grown in the presence of T2C feature strong electron density for a 5-membered ring species resembling l-T2C covalently bound to the N5 of the FAD in the PRODH domain. The modified FAD exhibits a large butterfly bend angle, indicating that the FAD is locked into the 2-electron reduced state. Reduction of the FAD is consistent with the crystals lacking the distinctive yellow color of the oxidized enzyme and stopped-flow kinetic data showing that T2C is a substrate for the PRODH domain of PutA. A mechanism is proposed in which PRODH catalyzes the oxidation of T2C at the C atom adjacent to the S atom of the thiazolidine ring (C5). Then, the N5 atom of the reduced FAD attacks the C5 of the oxidized T2C species, resulting in the covalent adduct observed in the crystal structure. To our knowledge, this is the first report of T2C inactivating (or inhibiting) PRODH or any other flavoenzyme. These results may inform the design of new mechanism-based inactivators of PRODH for use as chemical probes to study the roles of proline metabolism in cancer.
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Affiliation(s)
- Ashley C. Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Kent S. Gates
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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12
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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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13
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Scott GK, Yau C, Becker BC, Khateeb S, Mahoney S, Jensen MB, Hann B, Cowen BJ, Pegan SD, Benz CC. Targeting Mitochondrial Proline Dehydrogenase with a Suicide Inhibitor to Exploit Synthetic Lethal Interactions with p53 Upregulation and Glutaminase Inhibition. Mol Cancer Ther 2019; 18:1374-1385. [PMID: 31189611 PMCID: PMC6679736 DOI: 10.1158/1535-7163.mct-18-1323] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/05/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
Proline dehydrogenase (PRODH) is a p53-inducible inner mitochondrial membrane flavoprotein linked to electron transport for anaplerotic glutamate and ATP production, most critical for cancer cell survival under microenvironmental stress conditions. Proposing that PRODH is a unique mitochondrial cancer target, we structurally model and compare its cancer cell activity and consequences upon exposure to either a reversible (S-5-oxo: S-5-oxo-2-tetrahydrofurancarboxylic acid) or irreversible (N-PPG: N-propargylglycine) PRODH inhibitor. Unlike 5-oxo, the suicide inhibitor N-PPG induces early and selective decay of PRODH protein without triggering mitochondrial destruction, consistent with N-PPG activation of the mitochondrial unfolded protein response. Fly and breast tumor (MCF7)-xenografted mouse studies indicate that N-PPG doses sufficient to phenocopy PRODH knockout and induce its decay can be safely and effectively administered in vivo Among breast cancer cell lines and tumor samples, PRODH mRNA expression is subtype dependent and inversely correlated with glutaminase (GLS1) expression; combining inhibitors of PRODH (S-5-oxo and N-PPG) and GLS1 (CB-839) produces additive if not synergistic loss of cancer cell (ZR-75-1, MCF7, DU4475, and BT474) growth and viability. Although PRODH knockdown alone can induce cancer cell apoptosis, the anticancer potential of either reversible or irreversible PRODH inhibitors is strongly enhanced when p53 is simultaneously upregulated by an MDM2 antagonist (MI-63 and nutlin-3). However, maximum anticancer synergy is observed in vitro when the PRODH suicide inhibitor, N-PPG, is combined with both GLS1-inhibiting and a p53-upregulating MDM2 antagonist. These findings provide preclinical rationale for the development of N-PPG-like PRODH inhibitors as cancer therapeutics to exploit synthetic lethal interactions with p53 upregulation and GLS1 inhibition.
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Affiliation(s)
- Gary K Scott
- Buck Institute for Research on Aging, Novato, California
| | - Christina Yau
- Buck Institute for Research on Aging, Novato, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | - Sana Khateeb
- Buck Institute for Research on Aging, Novato, California
| | - Sophia Mahoney
- Buck Institute for Research on Aging, Novato, California
| | | | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Bryan J Cowen
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Scott D Pegan
- Center for Drug Discovery, College of Pharmacy, University of Georgia, Athens, Georgia
| | - Christopher C Benz
- Buck Institute for Research on Aging, Novato, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
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14
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Christgen SL, Becker DF. Role of Proline in Pathogen and Host Interactions. Antioxid Redox Signal 2019; 30:683-709. [PMID: 29241353 PMCID: PMC6338583 DOI: 10.1089/ars.2017.7335] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/26/2017] [Accepted: 11/14/2017] [Indexed: 01/20/2023]
Abstract
SIGNIFICANCE Proline metabolism has complex roles in a variety of biological processes, including cell signaling, stress protection, and energy production. Proline also contributes to the pathogenesis of various disease-causing organisms. Understanding the mechanisms of how pathogens utilize proline is important for developing new strategies against infectious diseases. Recent Advances: The ability of pathogens to acquire amino acids is critical during infection. Besides protein biosynthesis, some amino acids, such as proline, serve as a carbon, nitrogen, or energy source in bacterial and protozoa pathogens. The role of proline during infection depends on the physiology of the host/pathogen interactions. Some pathogens rely on proline as a critical respiratory substrate, whereas others exploit proline for stress protection. CRITICAL ISSUES Disruption of proline metabolism and uptake has been shown to significantly attenuate virulence of certain pathogens, whereas in other pathogens the importance of proline during infection is not known. Inhibiting proline metabolism and transport may be a useful therapeutic strategy against some pathogens. Developing specific inhibitors to avoid off-target effects in the host, however, will be challenging. Also, potential treatments that target proline metabolism should consider the impact on intracellular levels of Δ1-pyrroline-5-carboxylate, a metabolite intermediate that can have opposing effects on pathogenesis. FUTURE DIRECTIONS Further characterization of how proline metabolism is regulated during infection would provide new insights into the role of proline in pathogenesis. Biochemical and structural characterization of proline metabolic enzymes from different pathogens could lead to new tools for exploring proline metabolism during infection and possibly new therapeutic compounds.
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Affiliation(s)
- Shelbi L. Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska−Lincoln, Lincoln, Nebraska
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska−Lincoln, Lincoln, Nebraska
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15
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Abstract
SIGNIFICANCE Proline catabolism refers to the 4-electron oxidation of proline to glutamate catalyzed by the enzymes proline dehydrogenase (PRODH) and l-glutamate γ-semialdehyde dehydrogenase (GSALDH, or ALDH4A1). These enzymes and the intermediate metabolites of the pathway have been implicated in tumor growth and suppression, metastasis, hyperprolinemia metabolic disorders, schizophrenia susceptibility, life span extension, and pathogen virulence and survival. In some bacteria, PRODH and GSALDH are combined into a bifunctional enzyme known as proline utilization A (PutA). PutAs are not only virulence factors in some pathogenic bacteria but also fascinating systems for studying the coordination of metabolic enzymes via substrate channeling. Recent Advances: The past decade has seen an explosion of structural data for proline catabolic enzymes. This review surveys these structures, emphasizing protein folds, substrate recognition, oligomerization, kinetic mechanisms, and substrate channeling in PutA. CRITICAL ISSUES Major unsolved structural targets include eukaryotic PRODH, the complex between monofunctional PRODH and monofunctional GSALDH, and the largest of all PutAs, trifunctional PutA. The structural basis of PutA-membrane association is poorly understood. Fundamental aspects of substrate channeling in PutA remain unknown, such as the identity of the channeled intermediate, how the tunnel system is activated, and the roles of ancillary tunnels. FUTURE DIRECTIONS New approaches are needed to study the molecular and in vivo mechanisms of substrate channeling. With the discovery of the proline cycle driving tumor growth and metastasis, the development of inhibitors of proline metabolic enzymes has emerged as an exciting new direction. Structural biology will be important in these endeavors.
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Affiliation(s)
- John J Tanner
- 1 Department of Biochemistry and University of Missouri-Columbia , Columbia, Missouri.,2 Department of Chemistry, University of Missouri-Columbia , Columbia, Missouri
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16
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Liu LK, Tanner JJ. Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer. J Mol Biol 2018; 431:524-541. [PMID: 30529746 DOI: 10.1016/j.jmb.2018.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022]
Abstract
The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD+-dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the superfamily, owing to its extra C-terminal domain of unknown function and the absence of the essential catalytic cysteine residue in certain non-bacterial ALDH16 sequences. Herein we report the first production of recombinant ALDH16, the first biochemical characterization of ALDH16, and the first crystal structure of ALDH16. Recombinant expression systems were generated for the bacterial ALDH16 from Loktanella sp. and human ALDH16A1. Four high-resolution crystal structures of Loktanella ALDH16 were determined. Loktanella ALDH16 is found to be a bona fide enzyme, exhibiting NAD+-binding, ALDH activity, and esterase activity. In contrast, human ALDH16A1 apparently lacks measurable aldehyde oxidation activity, suggesting that it is a pseudoenzyme, consistent with the absence of the catalytic Cys in its sequence. The fold of ALDH16 comprises three domains: NAD+-binding, catalytic, and C-terminal. The latter is unique to ALDH16 and features a Rossmann fold connected to a protruding β-flap. The tertiary structural interactions of the C-terminal domain mimic the quaternary structural interactions of the classic ALDH superfamily dimer, a phenomenon we call "trans-hierarchical structural similarity." ALDH16 forms a unique dimer in solution, which mimics the classic ALDH superfamily dimer-of-dimer tetramer. Small-angle X-ray scattering shows that human ALDH16A1 has the same dimeric structure and fold as Loktanella ALDH16. We suggest that the Loktanella ALDH16 structure may be considered to be the archetype of the ALDH16 family.
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Affiliation(s)
- Li-Kai Liu
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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17
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Abstract
Interest in how proline contributes to cancer biology is expanding because of the emerging role of a novel proline metabolic cycle in cancer cell survival, proliferation, and metastasis. Proline biosynthesis and degradation involve the shared intermediate Δ1-pyrroline-5-carboxylate (P5C), which forms l-glutamate-γ-semialdehyde (GSAL) in a reversible non-enzymatic reaction. Proline is synthesized from glutamate or ornithine through GSAL/P5C, which is reduced to proline by P5C reductase (PYCR) in a NAD(P)H-dependent reaction. The degradation of proline occurs in the mitochondrion and involves two oxidative steps catalyzed by proline dehydrogenase (PRODH) and GSAL dehydrogenase (GSALDH). PRODH is a flavin-dependent enzyme that couples proline oxidation with reduction of membrane-bound quinone, while GSALDH catalyzes the NAD+-dependent oxidation of GSAL to glutamate. PRODH and PYCR form a metabolic relationship known as the proline-P5C cycle, a novel pathway that impacts cellular growth and death pathways. The proline-P5C cycle has been implicated in supporting ATP production, protein and nucleotide synthesis, anaplerosis, and redox homeostasis in cancer cells. This Perspective details the structures and reaction mechanisms of PRODH and PYCR and the role of the proline-P5C cycle in cancer metabolism. A major challenge in the field is to discover inhibitors that specifically target PRODH and PYCR isoforms for use as tools for studying proline metabolism and the functions of the proline-P5C cycle in cancer. These molecular probes could also serve as lead compounds in cancer drug discovery targeting the proline-P5C cycle.
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Affiliation(s)
- 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
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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18
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Korasick DA, Tanner JJ. Determination of protein oligomeric structure from small-angle X-ray scattering. Protein Sci 2018; 27:814-824. [PMID: 29352739 DOI: 10.1002/pro.3376] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/09/2022]
Abstract
Small-angle X-ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer. This approach is especially robust when the crystal structure of the target protein is known, and the candidate oligomer models are derived from the crystal lattice. When SAXS data are obtained at multiple protein concentrations, this analysis can provide insight into dynamic self-association equilibria. Herein, we summarize the computational methods that are used to determine protein molecular mass and quaternary structure from SAXS data. These methods are organized into a workflow and demonstrated with four case studies using experimental SAXS data from the published literature.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, 65211.,Department of Chemistry, University of Missouri, Columbia, Missouri, 65211
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19
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Aučynaitė A, Rutkienė R, Gasparavičiūtė R, Meškys R, Urbonavičius J. A gene encoding a DUF523 domain protein is involved in the conversion of 2-thiouracil into uracil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:49-56. [PMID: 29194984 DOI: 10.1111/1758-2229.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Modified nucleotides are present in many RNA species in all Domains of Life. While the biosynthetic pathways of such nucleotides are well studied, much less is known about the degradation of RNAs and the return to the metabolism of modified nucleotides, their respective nucleosides or heterocyclic bases. Using an E. coli uracil auxotroph, we screened the metagenomic libraries for genes, which would allow the conversion of 2-thiouracil to uracil and thereby lead to the growth on a defined synthetic medium. We show that a gene encoding a protein consisting of previously uncharacterized Domain of Unknown Function 523 (DUF523) is responsible for such phenotype. We have purified this recombinant protein and demonstrated that it contains a FeS cluster. The substitution of cysteines, which have been predicted to form such clusters, with alanines abolished the growth phenotype. We conclude that DUF523 is involved in the conversion of 2-thiouracil into uracil in vivo.
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Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
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20
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Korasick DA, Pemberton TA, Arentson BW, Becker DF, Tanner JJ. Structural Basis for the Substrate Inhibition of Proline Utilization A by Proline. Molecules 2017; 23:molecules23010032. [PMID: 29295473 PMCID: PMC5786444 DOI: 10.3390/molecules23010032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
Proline utilization A (PutA) is a bifunctional flavoenzyme that catalyzes the two-step oxidation of l-proline to l-glutamate using spatially separated proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) active sites. Substrate inhibition of the coupled PRODH-GSALDH reaction by proline is a common kinetic feature of PutAs, yet the structural basis for this phenomenon remains unknown. To understand the mechanism of substrate inhibition, we determined the 2.15 Å resolution crystal structure of Bradyrhizobium japonicum PutA complexed with proline. Proline was discovered in five locations remote from the PRODH active site. Most notably, strong electron density indicated that proline bound tightly to the GSAL binding site of the GSALDH active site. The pose and interactions of proline bound in this site are remarkably similar to those of the natural aldehyde substrate, GSAL, implying that proline inhibits the GSALDH reaction of PutA. Kinetic measurements show that proline is a competitive inhibitor of the PutA GSALDH reaction. Together, the structural and kinetic data show that substrate inhibition of the PutA coupled reaction is due to proline binding in the GSAL site.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Travis A Pemberton
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Benjamin W Arentson
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA.
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA.
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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21
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Schwander T, McLean R, Zarzycki J, Erb TJ. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J Biol Chem 2017; 293:1702-1712. [PMID: 29275330 PMCID: PMC5798300 DOI: 10.1074/jbc.ra117.000764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to α,β-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 Å. The enzyme forms a homodimer of two 60-kDa subunits. Compared with other ACDs, MCD contains an ∼170-residue-long N-terminal extension that structurally mimics a dimer–dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an α-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homolog of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD toward succinyl-CoA through active-site mutagenesis.
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Affiliation(s)
- Thomas Schwander
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Richard McLean
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Jan Zarzycki
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Tobias J Erb
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and .,the LOEWE Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
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22
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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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23
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Korasick DA, Singh H, Pemberton TA, Luo M, Dhatwalia R, Tanner JJ. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure. FEBS J 2017; 284:3029-3049. [PMID: 28710792 PMCID: PMC5603418 DOI: 10.1111/febs.14165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/06/2017] [Accepted: 07/12/2017] [Indexed: 01/07/2023]
Abstract
Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs. ENZYMES Proline dehydrogenase (EC 1.5.5.2); l-glutamate-γ-semialdehyde dehydrogenase (EC 1.2.1.88). DATABASES The atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank under accession number 5UR2. The SAXS data have been deposited in the SASBDB under the following accession codes: SASDCP3 (BbPutA), SASDCQ3 (DvPutA 1.5 mg·mL-1 ), SASDCX3 (DvPutA 3.0 mg·mL-1 ), SASDCY3 (DvPutA 4.5 mg·mL-1 ), SASDCR3 (LpPutA 3.0 mg·mL-1 ), SASDCV3 (LpPutA 5.0 mg·mL-1 ), SASDCW3 (LpPutA 8.0 mg·mL-1 ), SASDCS3 (BjPutA 2.3 mg·mL-1 ), SASDCT3 (BjPutA 4.7 mg·mL-1 ), SASDCU3 (BjPutA 7.0 mg·mL-1 ), SASDCZ3 (R51E 2.3 mg·mL-1 ), SASDC24 (R51E 4.7 mg·mL-1 ), SASDC34 (R51E 7.0 mg·mL-1 ).
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Affiliation(s)
- David A. Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, United States
| | - Harkewal Singh
- Department of Chemistry, University of Missouri, Columbia, MO 65211, United States
| | - Travis A. Pemberton
- Department of Chemistry, University of Missouri, Columbia, MO 65211, United States
| | - Min Luo
- Department of Chemistry, University of Missouri, Columbia, MO 65211, United States
| | - Richa Dhatwalia
- Department of Chemistry, University of Missouri, Columbia, MO 65211, 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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24
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Caudill MT, Budnick JA, Sheehan LM, Lehman CR, Purwantini E, Mukhopadhyay B, Caswell CC. Proline utilization system is required for infection by the pathogenic α-proteobacterium Brucella abortus. MICROBIOLOGY-SGM 2017; 163:970-979. [PMID: 28691659 DOI: 10.1099/mic.0.000490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proline utilization (Put) systems have been described in a number of bacteria; however, the importance and functionality of the Put system in the intracellular pathogen Brucellaabortus has not been explored. Generally, bacterial Put systems are composed of the bifunctional enzyme proline dehydrogenase PutA and its transcriptional activator PutR. Here, we demonstrate that the genes putA (bab2_0518) and putR (bab2_0517) are critical for the chronic infection of mice by B. abortus, but putA and putR are not required for the survival and replication of the bacteria in naive macrophages. Additionally, in vitro experiments revealed that putR is necessary for the ability of the bacteria to withstand oxidative stress, as a ΔputR deletion strain is hypersensitive to hydrogen peroxide exposure. Quantitative reverse transcription-PCR and putA-lacZ transcriptional reporter studies revealed that PutR acts as a transcriptional activator of putA in Brucella, and electrophoretic mobility shift assays confirmed that PutR binds directly to the putA promoter region. Biochemical analyses demonstrated that a purified recombinant B. abortus PutA protein possesses quintessential proline dehydrogenase activity, as PutA is capable of catalysing the conversion of proline to glutamate. Altogether, these data are the first to reveal that the Put system plays a significant role in the ability of B. abortus to replicate and survive within its host, as well as to describe the genetic regulation and biochemical activity of the Put system in Brucella.
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Affiliation(s)
- Mitchell T Caudill
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
| | - James A Budnick
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
| | - Lauren M Sheehan
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
| | - Christian R Lehman
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Clayton C Caswell
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24060, USA
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25
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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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Korasick DA, Gamage TT, Christgen S, Stiers KM, Beamer LJ, Henzl MT, Becker DF, Tanner JJ. Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis. J Biol Chem 2017; 292:9652-9665. [PMID: 28420730 PMCID: PMC5465489 DOI: 10.1074/jbc.m117.786855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/12/2017] [Indexed: 12/23/2022] Open
Abstract
The bifunctional flavoenzyme proline utilization A (PutA) catalyzes the two-step oxidation of proline to glutamate using separate proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase active sites. Because PutAs catalyze sequential reactions, they are good systems for studying how metabolic enzymes communicate via substrate channeling. Although mechanistically similar, PutAs vary widely in domain architecture, oligomeric state, and quaternary structure, and these variations represent different structural solutions to the problem of sequestering a reactive metabolite. Here, we studied PutA from Corynebacterium freiburgense (CfPutA), which belongs to the uncharacterized 3B class of PutAs. A 2.7 Å resolution crystal structure showed the canonical arrangement of PRODH, l-glutamate-γ-semialdehyde dehydrogenase, and C-terminal domains, including an extended interdomain tunnel associated with substrate channeling. The structure unexpectedly revealed a novel open conformation of the PRODH active site, which is interpreted to represent the non-activated conformation, an elusive form of PutA that exhibits suboptimal channeling. Nevertheless, CfPutA exhibited normal substrate-channeling activity, indicating that it isomerizes into the active state under assay conditions. Sedimentation-velocity experiments provided insight into the isomerization process, showing that CfPutA dimerizes in the presence of a proline analog and NAD+ These results are consistent with the morpheein model of enzyme hysteresis, in which substrate binding induces conformational changes that promote assembly of a high-activity oligomer. Finally, we used domain deletion analysis to investigate the function of the C-terminal domain. Although this domain contains neither catalytic residues nor substrate sites, its removal impaired both catalytic activities, suggesting that it may be essential for active-site integrity.
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Affiliation(s)
| | | | - Shelbi Christgen
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | | | | | | | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - John J Tanner
- From the Departments of Biochemistry and
- Chemistry, University of Missouri, Columbia, Missouri 65211, and
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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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