1
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Shabalin IG, Gritsunov A, Hou J, Sławek J, Miks CD, Cooper DR, Minor W, Christendat D. Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain. FEBS J 2019; 287:2235-2255. [PMID: 31750992 DOI: 10.1111/febs.15150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 01/19/2023]
Abstract
Tyrosine biosynthesis via the shikimate pathway is absent in humans and other animals, making it an attractive target for next-generation antibiotics, which is increasingly important due to the looming proliferation of multidrug-resistant pathogens. Tyrosine biosynthesis is also of commercial importance for the environmentally friendly production of numerous compounds, such as pharmaceuticals, opioids, aromatic polymers, and petrochemical aromatics. Prephenate dehydrogenase (PDH) catalyzes the penultimate step of tyrosine biosynthesis in bacteria: the oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate. The majority of PDHs are competitively inhibited by tyrosine and consist of a nucleotide-binding domain and a dimerization domain. Certain PDHs, including several from pathogens on the World Health Organization priority list of antibiotic-resistant bacteria, possess an additional ACT domain. However, biochemical and structural knowledge was lacking for these enzymes. In this study, we successfully established a recombinant protein expression system for PDH from Bacillus anthracis (BaPDH), the causative agent of anthrax, and determined the structure of a BaPDH ternary complex with NAD+ and tyrosine, a binary complex with tyrosine, and a structure of an isolated ACT domain dimer. We also conducted detailed kinetic and biophysical analyses of the enzyme. We show that BaPDH is allosterically regulated by tyrosine binding to the ACT domains, resulting in an asymmetric conformation of the BaDPH dimer that sterically prevents prephenate binding to either active site. The presented mode of allosteric inhibition is unique compared to both the competitive inhibition established for other PDHs and to the allosteric mechanisms for other ACT-containing enzymes. This study provides new structural and mechanistic insights that advance our understanding of tyrosine biosynthesis in bacteria. ENZYMES: Prephenate dehydrogenase from Bacillus anthracis (PDH): EC database ID: 1.3.1.12. DATABASES: Coordinates and structure factors have been deposited in the Protein Data Bank (PDB) with accession numbers PDB ID: 6U60 (BaPDH complex with NAD+ and tyrosine), PDB ID: 5UYY (BaPDH complex with tyrosine), and PDB ID: 5V0S (BaPDH isolated ACT domain dimer). The diffraction images are available at http://proteindiffraction.org with DOIs: https://doi.org/10.18430/M35USC, https://doi.org/10.18430/M35UYY, and https://doi.org/10.18430/M35V0S.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Artyom Gritsunov
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
| | - Jing Hou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Joanna Sławek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Charles D Miks
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, USA
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
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2
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Lopez-Nieves S, Pringle A, Maeda HA. Biochemical characterization of TyrA dehydrogenases from Saccharomyces cerevisiae (Ascomycota) and Pleurotus ostreatus (Basidiomycota). Arch Biochem Biophys 2019; 665:12-19. [PMID: 30771296 DOI: 10.1016/j.abb.2019.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/30/2022]
Abstract
L-Tyrosine is an aromatic amino acid necessary for protein synthesis in all living organisms and a precursor of secondary (specialized) metabolites. In fungi, tyrosine-derived compounds are associated with virulence and defense (i.e. melanin production). However, how tyrosine is produced in fungi is not fully understood. Generally, tyrosine can be synthesized via two pathways: by prephenate dehydrogenase (TyrAp/PDH), a pathway found in most bacteria, or by arogenate dehydrogenase (TyrAa/ADH), a pathway found mainly in plants. Both enzymes require the cofactor NAD+ or NADP+ and typically are strongly feedback inhibited by tyrosine. Here, we biochemically characterized two TyrA enzymes from two distantly related fungi in the Ascomycota and Basidiomycota, Saccharomyces cerevisiae (ScTyrA/TYR1) and Pleurotus ostreatus (PoTyrA), respectively. We found that both enzymes favor the prephenate substrate and NAD+ cofactor in vitro. Interestingly, while PoTyrA was strongly inhibited by tyrosine, ScTyrA exhibited relaxed sensitivity to tyrosine inhibition. We further mutated ScTyrA at the amino acid residue that was previously shown to be involved in the substrate specificity of plant TyrAs; however, no changes in its substrate specificity were observed, suggesting that a different mechanism is involved in the TyrA substrate specificity of fungal TyrAs. The current findings provide foundational knowledge to further understand and engineer tyrosine-derived specialized pathways in fungi.
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Affiliation(s)
- Samuel Lopez-Nieves
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Anne Pringle
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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3
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Lopez-Nieves S, Yang Y, Timoneda A, Wang M, Feng T, Smith SA, Brockington SF, Maeda HA. Relaxation of tyrosine pathway regulation underlies the evolution of betalain pigmentation in Caryophyllales. THE NEW PHYTOLOGIST 2018; 217:896-908. [PMID: 28990194 DOI: 10.1111/nph.14822] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/25/2017] [Indexed: 05/19/2023]
Abstract
Diverse natural products are synthesized in plants by specialized metabolic enzymes, which are often lineage-specific and derived from gene duplication followed by functional divergence. However, little is known about the contribution of primary metabolism to the evolution of specialized metabolic pathways. Betalain pigments, uniquely found in the plant order Caryophyllales, are synthesized from the aromatic amino acid l-tyrosine (Tyr) and replaced the otherwise ubiquitous phenylalanine-derived anthocyanins. This study combined biochemical, molecular and phylogenetic analyses, and uncovered coordinated evolution of Tyr and betalain biosynthetic pathways in Caryophyllales. We found that Beta vulgaris, which produces high concentrations of betalains, synthesizes Tyr via plastidic arogenate dehydrogenases (TyrAa /ADH) encoded by two ADH genes (BvADHα and BvADHβ). Unlike BvADHβ and other plant ADHs that are strongly inhibited by Tyr, BvADHα exhibited relaxed sensitivity to Tyr. Also, Tyr-insensitive BvADHα orthologs arose during the evolution of betalain pigmentation in the core Caryophyllales and later experienced relaxed selection and gene loss in lineages that reverted from betalain to anthocyanin pigmentation, such as Caryophyllaceae. These results suggest that relaxation of Tyr pathway regulation increased Tyr production and contributed to the evolution of betalain pigmentation, highlighting the significance of upstream primary metabolic regulation for the diversification of specialized plant metabolism.
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Affiliation(s)
- Samuel Lopez-Nieves
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ya Yang
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Alfonso Timoneda
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Minmin Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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4
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Schenck CA, Men Y, Maeda HA. Conserved Molecular Mechanism of TyrA Dehydrogenase Substrate Specificity Underlying Alternative Tyrosine Biosynthetic Pathways in Plants and Microbes. Front Mol Biosci 2017; 4:73. [PMID: 29164132 PMCID: PMC5681985 DOI: 10.3389/fmolb.2017.00073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/24/2017] [Indexed: 12/03/2022] Open
Abstract
L-Tyrosine (Tyr) is an aromatic amino acid synthesized de novo in plants and microbes. In animals, Tyr must be obtained through their diet or synthesized from L-phenylalanine. In addition to protein synthesis, Tyr serves as the precursor of neurotransmitters (e.g., dopamine and epinephrine) in animals and of numerous plant natural products, which serve essential functions in both plants and humans (e.g., vitamin E and morphine). Tyr is synthesized via two alternative routes mediated by a TyrA family enzyme, prephenate, or arogenate dehydrogenase (PDH/TyrAp or ADH/TyrAa), typically found in microbes and plants, respectively. Although ADH activity is also found in some bacteria, the origin of arogenate-specific TyrAa enzymes is unknown. We recently identified an acidic Asp222 residue that confers ADH activity in plant TyrAs. In this study, structure-guided phylogenetic analyses identified bacterial homologs, closely-related to plant TyrAs, that also have an acidic 222 residue and ADH activity. A more distant archaeon TyrA that preferred PDH activity had a non-acidic Gln, whose substitution to Glu introduced ADH activity. These results indicate that the conserved molecular mechanism operated during the evolution of arogenate-specific TyrAa in both plants and microbes.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Yusen Men
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
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5
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Schenck CA, Holland CK, Schneider MR, Men Y, Lee SG, Jez JM, Maeda HA. Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants. Nat Chem Biol 2017; 13:1029-1035. [PMID: 28671678 DOI: 10.1038/nchembio.2414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 11/09/2022]
Abstract
L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrAp) or arogenate dehydrogenase (ADH, also known as TyrAa), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that defines TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cynthia K Holland
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Matthew R Schneider
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yusen Men
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Soon Goo Lee
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Shlaifer I, Quashie PK, Kim HY, Turnbull JL. Biochemical characterization of TyrA enzymes from Ignicoccus hospitalis and Haemophilus influenzae: A comparative study of the bifunctional and monofunctional dehydrogenase forms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:312-320. [PMID: 28025081 DOI: 10.1016/j.bbapap.2016.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/23/2016] [Accepted: 12/22/2016] [Indexed: 02/08/2023]
Abstract
Biosynthesis of l-tyrosine (l-Tyr) is directed by the interplay of two enzymes. Chorismate mutase (CM) catalyzes the rearrangement of chorismate to prephenate, which is then converted to hydroxyphenylpyruvate by prephenate dehydrogenase (PD). This work reports the first characterization of the independently expressed PD domain of bifunctional CM-PD from the crenarchaeon Ignicoccus hospitalis and the first functional studies of both full-length CM-PD and the PD domain from the bacterium Haemophilus influenzae. All proteins were hexa-histidine tagged, expressed in Escherichia coli and purified. Expression and purification of I. hospitalis CM-PD generated a degradation product identified as a PD fragment lacking the protein's first 80 residues, Δ80CM-PD. A comparable stable PD domain could also be generated by limited tryptic digestion of this bifunctional enzyme. Thus, Δ80CM-PD constructs were prepared in both organisms. CM-PD and Δ80CM-PD from both organisms were dimeric and displayed the predicted enzymatic activities and thermal stabilities in accord with their hyperthermophilic and mesophilic origins. In contrast with H. influenzae PD activity which was NAD+-specific and displayed >75% inhibition with 50μM l-Tyr, I. hospitalis PD demonstrated dual cofactor specificity with a preference for NADP+ and an insensitivity to l-Tyr. These properties are consistent with a model of the I. hospitalis PD domain based on the previously reported structure of the H. influenzae homolog. Our results highlight the similarities and differences between the archaeal and bacterial TyrA proteins and reveal that the PD activity of both prokaryotes can be successfully mapped to a functionally independent unit.
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Affiliation(s)
- Irina Shlaifer
- Department of Chemistry and Biochemistry and the Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B 1R6, Canada
| | - Peter Kojo Quashie
- Department of Chemistry and Biochemistry and the Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B 1R6, Canada
| | - Hyun Young Kim
- Department of Chemistry and Biochemistry and the Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B 1R6, Canada
| | - Joanne L Turnbull
- Department of Chemistry and Biochemistry and the Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B 1R6, Canada.
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7
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Shlaifer I, Turnbull JL. Characterization of two key enzymes for aromatic amino acid biosynthesis in symbiotic archaea. Extremophiles 2016; 20:503-14. [DOI: 10.1007/s00792-016-0840-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
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8
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Schenck CA, Chen S, Siehl DL, Maeda HA. Non-plastidic, tyrosine-insensitive prephenate dehydrogenases from legumes. Nat Chem Biol 2015; 11:52-7. [PMID: 25402771 DOI: 10.1038/nchembio.1693] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/19/2014] [Indexed: 11/09/2022]
Abstract
L-Tyrosine (Tyr) and its plant-derived natural products are essential in both plants and humans. In plants, Tyr is generally assumed to be synthesized in the plastids via arogenate dehydrogenase (TyrA(a), also known also ADH), which is strictly inhibited by L-Tyr. Using phylogenetic and expression analyses, together with recombinant enzyme and endogenous activity assays, we identified prephenate dehydrogenases (TyrA(p)s, also known as PDHs) from two legumes, Glycine max (soybean) and Medicago truncatula. The identified PDHs were phylogenetically distinct from canonical plant ADH enzymes, preferred prephenate to arogenate substrate, localized outside of the plastids and were not inhibited by L-Tyr. The results provide molecular evidence for the diversification of primary metabolic Tyr pathway via an alternative cytosolic PDH pathway in plants.
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Affiliation(s)
- Craig A Schenck
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Siyu Chen
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Identification of a metagenome-derived prephenate dehydrogenase gene from an alkaline-polluted soil microorganism. Antonie Van Leeuwenhoek 2013; 103:1209-19. [PMID: 23479063 DOI: 10.1007/s10482-013-9899-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 03/02/2013] [Indexed: 10/27/2022]
Abstract
A novel prephenate dehydrogenase gene designated pdhE-1 was cloned by sequence-based screening of a plasmid metagenomic library from uncultured alkaline-polluted microorganisms. The deduced amino acid sequence comparison and phylogenetic analysis indicated that PdhE-1 and other putative prephenate dehydrogenases were closely related. The putative prephenate dehydrogenase gene was subcloned into pETBlue-2 vector and overexpressed in Escherichia coli BL21(DE3) pLacI. The recombinant protein was purified to homogeneity. The maximum activity of the PdhE-1 protein occurred at pH 8.0 and 45 °C using prephenic acid as the substrate. The prephenate dehydrogenase had an apparent K m value of 0.87 mM, a V max value of 41.5 U/mg, a k cat value of 604.8/min and a k cat/K m value of 1.16 × 10(4)/mol/s. L-Tyrosine did not obviously inhibit the recombinant PdhE-1 protein. The identification of a metagnome-derived prephenate dehydrogenase provides novel material for studies and application of proteins involved in tyrosine biosynthesis.
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10
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Ku HK, Do NH, Song JS, Choi S, Yeon SH, Shin MH, Kim KJ, Park SR, Park IY, Kim SK, Lee SJ. Crystal structure of prephenate dehydrogenase from Streptococcus mutans. Int J Biol Macromol 2011; 49:761-6. [PMID: 21798280 DOI: 10.1016/j.ijbiomac.2011.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 07/11/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
Abstract
Prephenate dehydrogenase (PDH) is a bacterial enzyme that catalyzes conversion of prephenate to 4-hydroxyphenylpyruvate through the oxidative decarboxylation pathway for tyrosine biosynthesis. This enzymatic pathway exists in prokaryotes but is absent in mammals, indicating that it is a potential target for the development of new antibiotics. The crystal structure of PDH from Streptococcus mutans in a complex with NAD(+) shows that the enzyme exists as a homo-dimer, each monomer consisting of two domains, a modified nucleotide binding N-terminal domain and a helical prephenate C-terminal binding domain. The latter is the dimerization domain. A structural comparison of PDHs from mesophilic S. mutans and thermophilic Aquifex aeolicus showed differences in the long loop between β6 and β7, which may be a reason for the high K(m) values of PDH from Streptococcus mutans.
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Affiliation(s)
- Hyung-Keun Ku
- Division of Metrology for Quality of Life, Department of Bio-Analytical Science, University of Science & Technology, Daejeon, Republic of Korea
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11
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Chiu HJ, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1317-25. [PMID: 20944228 PMCID: PMC2954222 DOI: 10.1107/s1744309110021688] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 06/07/2010] [Indexed: 11/10/2022]
Abstract
Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)(+)-dependent oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD(+) has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α-β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP(+) and NAD(+). The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365' (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.
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Affiliation(s)
- Hsiu-Ju Chiu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debanu Das
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Anna Grzechnik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Piotr Kozbial
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Abhinav Kumar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry J. Tien
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine B. Trame
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Qingping Xu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Sanford–Burnham Medical Research Institute, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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12
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Ku HK, Park SR, Yang I, Kim SK. Expression and functional characterization of prephenate dehydrogenase from Streptococcus mutans. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Sun W, Shahinas D, Bonvin J, Hou W, Kimber MS, Turnbull J, Christendat D. The crystal structure of Aquifex aeolicus prephenate dehydrogenase reveals the mode of tyrosine inhibition. J Biol Chem 2009; 284:13223-32. [PMID: 19279014 DOI: 10.1074/jbc.m806272200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TyrA proteins belong to a family of dehydrogenases that are dedicated to l-tyrosine biosynthesis. The three TyrA subclasses are distinguished by their substrate specificities, namely the prephenate dehydrogenases, the arogenate dehydrogenases, and the cyclohexadienyl dehydrogenases, which utilize prephenate, l-arogenate, or both substrates, respectively. The molecular mechanism responsible for TyrA substrate selectivity and regulation is unknown. To further our understanding of TyrA-catalyzed reactions, we have determined the crystal structures of Aquifex aeolicus prephenate dehydrogenase bound with NAD(+) plus either 4-hydroxyphenylpyuvate, 4-hydroxyphenylpropionate, or l-tyrosine and have used these structures as guides to target active site residues for site-directed mutagenesis. From a combination of mutational and structural analyses, we have demonstrated that His-147 and Arg-250 are key catalytic and binding groups, respectively, and Ser-126 participates in both catalysis and substrate binding through the ligand 4-hydroxyl group. The crystal structure revealed that tyrosine, a known inhibitor, binds directly to the active site of the enzyme and not to an allosteric site. The most interesting finding though, is that mutating His-217 relieved the inhibitory effect of tyrosine on A. aeolicus prephenate dehydrogenase. The identification of a tyrosine-insensitive mutant provides a novel avenue for designing an unregulated enzyme for application in metabolic engineering.
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Affiliation(s)
- Warren Sun
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
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14
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Characterization of a key trifunctional enzyme for aromatic amino acid biosynthesis in Archaeoglobus fulgidus. Extremophiles 2008; 13:191-8. [PMID: 19082689 DOI: 10.1007/s00792-008-0209-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 11/10/2008] [Indexed: 10/21/2022]
Abstract
In the aromatic amino acid biosynthesis pathway, chorismate presents a branch point intermediate that is converted to tryptophan, phenylalanine (Phe), and tyrosine (Tyr). In bacteria, three enzymes catalyze the conversion of chorismate to hydroxyphenylpyruvate or pyruvate. The enzymes, chorismate mutase (CM), prephenate dehydratase (PDT), and prephenate dehydrogenase (PDHG) are either present as distinct proteins or fusions combining two activities. Gene locus AF0227 of Archaeoglobus fulgidus is predicted to encode a fusion protein, AroQ, containing all three enzymatic domains. This work describes the first characterization of a trifunctional AroQ. The A. fulgidus aroQ gene was cloned and overexpressed in Escherichia coli. The recombinant protein purified as a homohexamer with specific activities of 10, 0.51, and 50 U/mg for CM, PDT, and PDHG, respectively. Tyr at 0.5 mM concentration inhibited PDHG activity by 50%, while at 1 mM PDT was activated by 70%. Phe at 5 muM inhibited PDT activity by 66% without affecting the activity of PDHG. A fusion of CM, PDT, and PDHG domains is evident in the genome of only one other organism sequenced to date, that of the hyperthermophilic archaeon, Nanoarchaeum equitans. Such fusions of contiguous activities in a biosynthetic pathway may constitute a primitive strategy for the efficient processing of labile metabolites.
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15
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Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities. Microbiol Mol Biol Rev 2008; 72:13-53, table of contents. [PMID: 18322033 DOI: 10.1128/mmbr.00026-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.
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16
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Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA. Cohesion group approach for evolutionary analysis of TyrA, a protein family with wide-ranging substrate specificities. Microbiol Mol Biol Rev 2008. [PMID: 18322033 DOI: 10.1128/mmbr.00026-27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.
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Affiliation(s)
- Carol A Bonner
- The Computation Institute, University of Chicago, Chicago, Illinois 606371, USA
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