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Zmuda AJ, Kang X, Wissbroecker KB, Freund Saxhaug K, Costa KC, Hegeman AD, Niehaus TD. A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle. Nat Commun 2024; 15:846. [PMID: 38287013 PMCID: PMC10825186 DOI: 10.1038/s41467-024-45134-0] [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: 08/22/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
A prevalent side-reaction of succinate dehydrogenase oxidizes malate to enol-oxaloacetate (OAA), a metabolically inactive form of OAA that is a strong inhibitor of succinate dehydrogenase. We purified from cow heart mitochondria an enzyme (OAT1) with OAA tautomerase (OAT) activity that converts enol-OAA to the physiological keto-OAA form, and determined that it belongs to the highly conserved and previously uncharacterized Fumarylacetoacetate_hydrolase_domain-containing protein family. From all three domains of life, heterologously expressed proteins were shown to have strong OAT activity, and ablating the OAT1 homolog caused significant growth defects. In Escherichia coli, expression of succinate dehydrogenase was necessary for OAT1-associated growth defects to occur, and ablating OAT1 caused a significant increase in acetate and other metabolites associated with anaerobic respiration. OAT1 increased the succinate dehydrogenase reaction rate by 35% in in vitro assays with physiological concentrations of both succinate and malate. Our results suggest that OAT1 is a universal metabolite repair enzyme that is required to maximize aerobic respiration efficiency by preventing succinate dehydrogenase inhibition.
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Affiliation(s)
- Anthony J Zmuda
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Xiaojun Kang
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Katie B Wissbroecker
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Katrina Freund Saxhaug
- Department of Horticultural Science, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Adrian D Hegeman
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
- Department of Horticultural Science, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA.
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2
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Cheng HC, Chi SC, Liang CY, Yu JY, Wang AG. Candidate Modifier Genes for the Penetrance of Leber's Hereditary Optic Neuropathy. Int J Mol Sci 2022; 23:ijms231911891. [PMID: 36233195 PMCID: PMC9569928 DOI: 10.3390/ijms231911891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally transmitted disease caused by mitochondria DNA (mtDNA) mutation. It is characterized by acute and subacute visual loss predominantly affecting young men. The mtDNA mutation is transmitted to all maternal lineages. However, only approximately 50% of men and 10% of women harboring a pathogenic mtDNA mutation develop optic neuropathy, reflecting both the incomplete penetrance and its unexplained male prevalence, where over 80% of patients are male. Nuclear modifier genes have been presumed to affect the penetrance of LHON. With conventional genetic methods, prior studies have failed to solve the underlying pathogenesis. Whole exome sequencing (WES) is a new molecular technique for sequencing the protein-coding region of all genes in a whole genome. We performed WES from five families with 17 members. These samples were divided into the proband group (probands with acute onset of LHON, n = 7) and control group (carriers including mother and relative carriers with mtDNSA 11778 mutation, without clinical manifestation of LHON, n = 10). Through whole exome analysis, we found that many mitochondria related (MT-related) nuclear genes have high percentage of variants in either the proband group or control group. The MT genes with a difference over 0.3 of mutation percentage between the proband and control groups include AK4, NSUN4, RDH13, COQ3, and FAHD1. In addition, the pathway analysis revealed that these genes were associated with cofactor metabolism pathways. Family-based analysis showed that several candidate MT genes including METAP1D (c.41G > T), ACACB (c.1029del), ME3 (c.972G > C), NIPSNAP3B (c.280G > C, c.476C > G), and NSUN4 (c.4A > G) were involved in the penetrance of LHON. A GWAS (genome wide association study) was performed, which found that ADGRG5 (Chr16:575620A:G), POLE4 (Chr2:7495872T:G), ERMAP (Chr1:4283044A:G), PIGR (Chr1:2069357C:T;2069358G:A), CDC42BPB (Chr14:102949A:G), PROK1 (Chr1:1104562A:G), BCAN (Chr 1:1566582C:T), and NES (Chr1:1566698A:G,1566705T:C, 1566707T:C) may be involved. The incomplete penetrance and male prevalence are still the major unexplained issues in LHON. Through whole exome analysis, we found several MT genes with a high percentage of variants were involved in a family-based analysis. Pathway analysis suggested a difference in the mutation burden of MT genes underlining the biosynthesis and metabolism pathways. In addition, the GWAS analysis also revealed several candidate nuclear modifier genes. The new technology of WES contributes to provide a highly efficient candidate gene screening function in molecular genetics.
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Affiliation(s)
- Hui-Chen Cheng
- Program in Molecular Medicine, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sheng-Chu Chi
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
| | - Chiao-Ying Liang
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Jenn-Yah Yu
- Department of Life Sciences and Institute of Genome Sciences, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - An-Guor Wang
- Department of Ophthalmology, Taipei Veterans General Hospital, 201 Sec. 2, Shih-Pai Rd., Taipei 11217, Taiwan
- Department of Ophthalmology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: ; Tel.: +886-2-2875-7325; Fax: +886-2-2876-1351
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3
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Fujii H, Hibi M, Shimizu S, Yokozeki K, Ogawa J. Three enzymes of Rhizobium radiobacter involved in the novel metabolism of two naturally occurring bioactive oxidative derivatives of L-isoleucine. Biosci Biotechnol Biochem 2022; 86:1247-1254. [PMID: 35793557 DOI: 10.1093/bbb/zbac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]
Abstract
Rhizobium radiobacter C58 was found to convert 4-hydroxyisoleucine (HIL) and 2-amino-3-methyl-4-ketopentanoate (AMKP), bioactive oxidative derivatives of L-isoleucine, in both cases producing 2-aminobutyrate. Three native enzymes involved in these metabolisms were purified by column chromatography and successfully identified. In this strain, HIL was converted to acetaldehyde and 2-aminobutyrate by coupling action of the transaminase rrIlvE and the aldolase HkpA. AMKP was also converted to acetate and 2-aminobutyrate by coupling action of rrIlvE and a hydrolase DkhA. In the multi-enzymatic reactions, HkpA catalyzes the retro-aldol reaction of 4-hydroxy-3-methyl-2-ketopentanoate into acetaldehyde and 2-ketobutyrate, and DkhA catalyzes hydrolytic cleavage of the carbon-carbon bond of 2,4-diketo-3-methylpentanoate into acetate and 2-ketobutyrate. And rrIlvE catalyzes reversible transamination between HIL and 4-hydroxy-3-methyl-2-ketopentanoate, AMKP and 2,4-diketo-3-methylpentanoate, and 2-ketobutyrate and 2-aminobutyrate. The results suggested that the conversion activity of Rhizobium bacteria play an important role in the complex biological metabolic networks associated with HIL and AMKP.
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Affiliation(s)
- Hidemi Fujii
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Makoto Hibi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Kenzo Yokozeki
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan.,Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Suzuki-cho, Kawasaki-ku, Kawasaki, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
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4
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Gerna D, Arc E, Holzknecht M, Roach T, Jansen-Dürr P, Weiss AK, Kranner I. AtFAHD1a: A New Player Influencing Seed Longevity and Dormancy in Arabidopsis? Int J Mol Sci 2021; 22:2997. [PMID: 33804275 PMCID: PMC8001395 DOI: 10.3390/ijms22062997] [Citation(s) in RCA: 4] [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: 02/18/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) proteins form a superfamily found in Archaea, Bacteria, and Eukaryota. However, few fumarylacetoacetate hydrolase domain (FAHD)-containing proteins have been studied in Metazoa and their role in plants remains elusive. Sequence alignments revealed high homology between two Arabidopsis thaliana FAHD-containing proteins and human FAHD1 (hFAHD1) implicated in mitochondrial dysfunction-associated senescence. Transcripts of the closest hFAHD1 orthologue in Arabidopsis (AtFAHD1a) peak during seed maturation drying, which influences seed longevity and dormancy. Here, a homology study was conducted to assess if AtFAHD1a contributes to seed longevity and vigour. We found that an A. thaliana T-DNA insertional line (Atfahd1a-1) had extended seed longevity and shallower thermo-dormancy. Compared to the wild type, metabolite profiling of dry Atfahd1a-1 seeds showed that the concentrations of several amino acids, some reducing monosaccharides, and δ-tocopherol dropped, whereas the concentrations of dehydroascorbate, its catabolic intermediate threonic acid, and ascorbate accumulated. Furthermore, the redox state of the glutathione disulphide/glutathione couple shifted towards a more reducing state in dry mature Atfahd1a-1 seeds, suggesting that AtFAHD1a affects antioxidant redox poise during seed development. In summary, AtFAHD1a appears to be involved in seed redox regulation and to affect seed quality traits such as seed thermo-dormancy and longevity.
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Affiliation(s)
- Davide Gerna
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; (E.A.); (T.R.); (I.K.)
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
| | - Erwann Arc
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; (E.A.); (T.R.); (I.K.)
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
| | - Max Holzknecht
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
- Research Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, 6020 Innsbruck, Austria
| | - Thomas Roach
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; (E.A.); (T.R.); (I.K.)
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
| | - Pidder Jansen-Dürr
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
- Research Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, 6020 Innsbruck, Austria
| | - Alexander K.H. Weiss
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
- Research Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, 6020 Innsbruck, Austria
| | - Ilse Kranner
- Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria; (E.A.); (T.R.); (I.K.)
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria; (M.H.); (P.J.-D.)
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5
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Weiss AKH, Albertini E, Holzknecht M, Cappuccio E, Dorigatti I, Krahbichler A, Damisch E, Gstach H, Jansen-Dürr P. Regulation of cellular senescence by eukaryotic members of the FAH superfamily - A role in calcium homeostasis? Mech Ageing Dev 2020; 190:111284. [PMID: 32574647 PMCID: PMC7116474 DOI: 10.1016/j.mad.2020.111284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 01/04/2023]
Abstract
Fumarylacetoacetate hydrolase (FAH) superfamily members are commonly expressed in the prokaryotic kingdom, where they take part in the committing steps of degradation pathways of complex carbon sources. Besides FAH itself, the only described FAH superfamily members in the eukaryotic kingdom are fumarylacetoacetate hydrolase domain containing proteins (FAHD) 1 and 2, that have been a focus of recent work in aging research. Here, we provide a review of current knowledge on FAHD proteins. Of those, FAHD1 has recently been described as a regulator of mitochondrial function and senescence, in the context of mitochondrial dysfunction associated senescence (MiDAS). This work further describes data based on bioinformatics analysis, 3D structure comparison and sequence alignment, that suggests a putative role of FAHD proteins as calcium binding proteins.
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Affiliation(s)
- Alexander K H Weiss
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria.
| | - Eva Albertini
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Max Holzknecht
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Elia Cappuccio
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Ilaria Dorigatti
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Anna Krahbichler
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Elisabeth Damisch
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
| | - Hubert Gstach
- University of Vienna, UZ2 E349, Department of Pharmaceutical Chemistry, Faculty of Life Sciences, Althanstrasse 14, 1090, Vienna, Austria
| | - Pidder Jansen-Dürr
- University of Innsbruck, Research Institute for Biomedical Aging Research, Rennweg 10, A-6020, Innsbruck, Austria; University of Innsbruck, Center for Molecular Biosciences Innsbruck (CMBI), Austria
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6
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Hong H, Seo H, Park W, Kim KJ. Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies. Environ Microbiol 2019; 22:270-285. [PMID: 31657110 DOI: 10.1111/1462-2920.14844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 11/30/2022]
Abstract
Fumarylacetoacetate hydrolase (FAH) superfamily proteins are found ubiquitously in microbial pathways involved in the catabolism of aromatic substances. Although extensive bioinformatic data on these proteins have been acquired, confusion caused by problems with the annotation of these proteins hinders research into determining their physiological functions. Here we classify 606 FAH superfamily proteins using a maximum likelihood (ML) phylogenetic tree, comparative gene-neighbourhood patterns and in vitro enzyme assays. The FAH superfamily proteins used for the analyses are divided into five distinct subfamilies, and two of them, FPH-A and FPH-B, contain the majority of the proteins of undefined function. These subfamilies include clusters designated FPH-I and FPH-II, respectively, which include two distinct types of fumarylpyruvate hydrolase (FPH), an enzyme involved in the final step of the gentisate pathway. We determined the crystal structures of these FPH enzymes at 2.0 Å resolutions and investigate the substrate binding mode by which these types of enzymes can accommodate fumarylpyruvate as a substrate. Consequentially, we identify the molecular signatures of the two types of FPH enzymes among the broadly conserved FAH superfamily proteins. Our studies allowed us to predict the relationship of unknown FAH superfamily proteins using their sequence information.
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Affiliation(s)
- Hwaseok Hong
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Hogyun Seo
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Woojin Park
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
| | - Kyung-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 702701, Republic of Korea.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 702701, Republic of Korea
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7
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Macias I, Laín A, Bernardo-Seisdedos G, Gil D, Gonzalez E, Falcon-Perez JM, Millet O. Hereditary tyrosinemia type I-associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate. J Biol Chem 2019; 294:13051-13060. [PMID: 31300554 PMCID: PMC6721957 DOI: 10.1074/jbc.ra119.009367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/11/2019] [Indexed: 12/11/2022] Open
Abstract
More than 100 mutations in the gene encoding fumarylacetoacetate hydrolase (FAH) cause hereditary tyrosinemia type I (HT1), a metabolic disorder characterized by elevated blood levels of tyrosine. Some of these mutations are known to decrease FAH catalytic activity, but the mechanisms of FAH mutation–induced pathogenicity remain poorly understood. Here, using diffusion ordered NMR spectroscopy, cryo-EM, and CD analyses, along with site-directed mutagenesis, enzymatic assays, and molecular dynamics simulations, we investigated the putative role of thermodynamic and kinetic stability in WT FAH and a representative set of 19 missense mutations identified in individuals with HT1. We found that at physiological temperatures and concentrations, WT FAH is in equilibrium between a catalytically active dimer and a monomeric species, with the latter being inactive and prone to oligomerization and aggregation. We also found that the majority of the deleterious mutations reduce the kinetic stability of the enzyme and always accelerate the FAH aggregation pathway. Depending mainly on the position of the amino acid in the structure, pathogenic mutations either reduced the dimer population or decreased the energy barrier that separates the monomer from the aggregate. The mechanistic insights reported here pave the way for the development of pharmacological chaperones that target FAH to tackle the severe disease HT1.
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Affiliation(s)
- Iratxe Macias
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ana Laín
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Ganeko Bernardo-Seisdedos
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - David Gil
- Electron Microscopy Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Esperanza Gonzalez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Juan M Falcon-Perez
- Exosomes Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, 48013 Spain
| | - Oscar Millet
- Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain.
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8
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Weiss AKH, Holzknecht M, Cappuccio E, Dorigatti I, Kreidl K, Naschberger A, Rupp B, Gstach H, Jansen-Dürr P. Expression, Purification, Crystallization, and Enzyme Assays of Fumarylacetoacetate Hydrolase Domain-Containing Proteins. J Vis Exp 2019:10.3791/59729. [PMID: 31282888 PMCID: PMC7115867 DOI: 10.3791/59729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) domain-containing proteins (FAHD) are identified members of the FAH superfamily in eukaryotes. Enzymes of this superfamily generally display multi-functionality, involving mainly hydrolase and decarboxylase mechanisms. This article presents a series of consecutive methods for the expression and purification of FAHD proteins, mainly FAHD protein 1 (FAHD1) orthologues among species (human, mouse, nematodes, plants, etc.). Covered methods are protein expression in E. coli, affinity chromatography, ion exchange chromatography, preparative and analytical gel filtration, crystallization, X-ray diffraction, and photometric assays. Concentrated protein of high levels of purity (>98%) may be employed for crystallization or antibody production. Proteins of similar or lower quality may be employed in enzyme assays or used as antigens in detection systems (Western-Blot, ELISA). In the discussion of this work, the identified enzymatic mechanisms of FAHD1 are outlined to describe its hydrolase and decarboxylase bi-functionality in more detail.
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Affiliation(s)
- Alexander K H Weiss
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck Austria;
| | - Max Holzknecht
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck Austria
| | - Elia Cappuccio
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck Austria
| | - Ilaria Dorigatti
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria
| | - Karin Kreidl
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria
| | | | - Bernhard Rupp
- Division of Genetic Epidemiology, Medical University of Innsbruck Austria
| | - Hubert Gstach
- Faculty of Chemistry, Department of Organic Chemistry, University of Vienna Austria
| | - Pidder Jansen-Dürr
- Research Institute for Biomedical Aging Research, University of Innsbruck Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck Austria
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9
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Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum. Biochem Biophys Res Commun 2019; 509:773-778. [PMID: 30630595 DOI: 10.1016/j.bbrc.2018.12.183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 12/30/2018] [Indexed: 11/23/2022]
Abstract
Fumarylacetoacetate hydrolase (FAH) is essential for the degradation of aromatic amino acids as well as for the cleavage of carbon-carbon bonds in metabolites or small organic compounds. Here, the X-ray crystal structure of EaFAH, a dimeric fumarylacetoacetate hydrolase from Exiguobacterium antarcticum, was determined, and its functional properties were investigated using biochemical methods. EaFAH adopts a mixed β-sandwich roll fold with a highly flexible lid region (Val73-Leu94), and an Mg2+ ion is bound at the active site by coordinating to the three carboxylate oxygen atoms of Glu124, Glu126, and Asp155. The hydrolytic activity of EaFAH toward various substrates, including linalyl acetate was investigated using native polyacrylamide gel electrophoresis, activity staining, gel filtration, circular dichroism spectroscopy, fluorescence, and enzyme assays.
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10
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Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1. Biochem J 2018; 475:3561-3576. [PMID: 30348641 DOI: 10.1042/bcj20180750] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 11/17/2022]
Abstract
Whereas enzymes in the fumarylacetoacetate hydrolase (FAH) superfamily catalyze several distinct chemical reactions, the structural basis for their multi-functionality remains elusive. As a well-studied example, human FAH domain-containing protein 1 (FAHD1) is a mitochondrial protein displaying both acylpyruvate hydrolase (ApH) and oxaloacetate decarboxylase (ODx) activity. As mitochondrial ODx, FAHD1 acts antagonistically to pyruvate carboxylase, a key metabolic enzyme. Despite its importance for mitochondrial function, very little is known about the catalytic mechanisms underlying FAHD1 enzymatic activities, and the architecture of its ligated active site is currently ill defined. We present crystallographic data of human FAHD1 that provide new insights into the structure of the catalytic center at high resolution, featuring a flexible 'lid'-like helical region which folds into a helical structure upon binding of the ODx inhibitor oxalate. The oxalate-driven structural transition results in the generation of a potential catalytic triad consisting of E33, H30 and an associated water molecule. In silico docking studies indicate that the substrate is further stabilized by a complex hydrogen-bond network, involving amino acids Q109 and K123, identified herein as potential key residues for FAHD1 catalytic activity. Mutation of amino acids H30, E33 and K123 each had discernible influence on the ApH and/or ODx activity of FAHD1, suggesting distinct catalytic mechanisms for both activities. The structural analysis presented here provides a defined structural map of the active site of FAHD1 and contributes to a better understanding of the FAH superfamily of enzymes.
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Guimarães SL, Coitinho JB, Costa DMA, Araújo SS, Whitman CP, Nagem RAP. Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid. Biochemistry 2016; 55:2632-45. [PMID: 27082660 DOI: 10.1021/acs.biochem.6b00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.
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Affiliation(s)
- Samuel L Guimarães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, 31270-901, Brazil
| | - Juliana B Coitinho
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, 31270-901, Brazil
| | - Débora M A Costa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, 31270-901, Brazil
| | - Simara S Araújo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, 31270-901, Brazil
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin , Texas 78712-1071, United States
| | - Ronaldo A P Nagem
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais , Belo Horizonte, 31270-901, Brazil
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Liu Y, Xia W, Yang P, Zhang S, Shi Z, Tang H, Zhang L. Cloning and expression of fumarylacetoacetate hydrolase derived from marine yeastRhodosporidium diobovatum. J Basic Microbiol 2015; 55:1082-93. [DOI: 10.1002/jobm.201400908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yuxuan Liu
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Weiwei Xia
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Pucheng Yang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Shuo Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Zhihui Shi
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Hui Tang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
| | - Liping Zhang
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province; College of Life Sciences; Hebei University; Baoding 071002 China
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Pircher H, von Grafenstein S, Diener T, Metzger C, Albertini E, Taferner A, Unterluggauer H, Kramer C, Liedl KR, Jansen-Dürr P. Identification of FAH domain-containing protein 1 (FAHD1) as oxaloacetate decarboxylase. J Biol Chem 2015; 290:6755-62. [PMID: 25575590 DOI: 10.1074/jbc.m114.609305] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) domain-containing proteins occur in both prokaryotes and eukaryotes, where they carry out diverse enzymatic reactions, probably related to structural differences in their respective FAH domains; however, the precise relationship between structure of the FAH domain and the associated enzyme function remains elusive. In mammals, three FAH domain-containing proteins, FAHD1, FAHD2A, and FAHD2B, are known; however, their enzymatic function, if any, remains to be demonstrated. In bacteria, oxaloacetate is subject to enzymatic decarboxylation; however, oxaloacetate decarboxylases (ODx) were so far not identified in eukaryotes. Based on molecular modeling and subsequent biochemical investigations, we identified FAHD1 as a eukaryotic ODx enzyme. The results presented here indicate that dedicated oxaloacetate decarboxylases exist in eukaryotes.
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Affiliation(s)
- Haymo Pircher
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Susanne von Grafenstein
- the Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas Diener
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Christina Metzger
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Eva Albertini
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Andrea Taferner
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Hermann Unterluggauer
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
| | - Christian Kramer
- the Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- the Institute for General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Pidder Jansen-Dürr
- From the Institute for Biomedical Aging Research and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Rennweg 10, 6020 Innsbruck and
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Crystal structures of Cg1458 reveal a catalytic lid domain and a common catalytic mechanism for the FAH family. Biochem J 2013; 449:51-60. [PMID: 23046410 DOI: 10.1042/bj20120913] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cg1458 was recently characterized as a novel soluble oxaloacetate decarboxylase. However, sequence alignment identified that Cg1458 has no similarity with other oxaloacetate decarboxylases and instead belongs to the FAH (fumarylacetoacetate hydrolase) family. Differences in the function of Cg1458 and other FAH proteins may suggest a different catalytic mechanism. To help elucidate the catalytic mechanism of Cg1458, crystal structures of Cg1458 in both the open and closed conformations have been determined for the first time up to a resolution of 1.9 Å (1 Å=0.1 nm) and 2.0 Å respectively. Comparison of both structures and detailed biochemical studies confirmed the presence of a catalytic lid domain which is missing in the native enzyme structure. In this lid domain, a glutamic acid-histidine dyad was found to be critical in mediating enzymatic catalysis. On the basis of structural modelling and comparison, as well as large-scale sequence alignment studies, we further determined that the catalytic mechanism of Cg1458 is actually through a glutamic acid-histidine-water triad, and this catalytic triad is common among FAH family proteins that catalyse the cleavage of the C-C bond of the substrate. Two sequence motifs, HxxE and Hxx…xxE have been identified as the basis for this mechanism.
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15
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Pircher H, Straganz GD, Ehehalt D, Morrow G, Tanguay RM, Jansen-Dürr P. Identification of human fumarylacetoacetate hydrolase domain-containing protein 1 (FAHD1) as a novel mitochondrial acylpyruvase. J Biol Chem 2011; 286:36500-8. [PMID: 21878618 PMCID: PMC3196145 DOI: 10.1074/jbc.m111.264770] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 08/25/2011] [Indexed: 11/16/2022] Open
Abstract
The human fumarylacetoacetate hydrolase (FAH) domain-containing protein 1 (FAHD1) is part of the FAH protein superfamily, but its enzymatic function is unknown. In the quest for a putative enzymatic function of FAHD1, we found that FAHD1 exhibits acylpyruvase activity, demonstrated by the hydrolysis of acetylpyruvate and fumarylpyruvate in vitro, whereas several structurally related compounds were not hydrolyzed as efficiently. Conserved amino acids Asp-102 and Arg-106 of FAHD1 were found important for its catalytic activity, and Mg(2+) was required for maximal enzyme activity. FAHD1 was found expressed in all tested murine tissues, with highest expression in liver and kidney. FAHD1 was also found in several human cell lines, where it localized to mitochondria. In summary, the current work identified mammalian FAHD1 as a novel mitochondrial enzyme with acylpyruvate hydrolase activity.
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Affiliation(s)
- Haymo Pircher
- From the Institute for Biomedical Aging Research, Austrian Academy of Sciences, A-6020 Innsbruck, Austria
| | - Grit D. Straganz
- the Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, A-8010 Graz, Austria, and
| | - Daniela Ehehalt
- From the Institute for Biomedical Aging Research, Austrian Academy of Sciences, A-6020 Innsbruck, Austria
| | - Geneviève Morrow
- the Laboratory of Cell and Developmental Genetics, Department of Molecular Biology, Medical Biochemistry and Pathology, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Robert M. Tanguay
- the Laboratory of Cell and Developmental Genetics, Department of Molecular Biology, Medical Biochemistry and Pathology, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Pidder Jansen-Dürr
- From the Institute for Biomedical Aging Research, Austrian Academy of Sciences, A-6020 Innsbruck, Austria
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Yun JH, Bong JJ, Myung K, Baik M. Correlations between carcass traits and mRNA levels of CGI-105 and CCAAT/enhancer protein α genes in steers of Korean cattle. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.06.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Brouns SJJ, Barends TRM, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J Mol Biol 2008; 379:357-71. [PMID: 18448118 DOI: 10.1016/j.jmb.2008.03.064] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 03/22/2008] [Accepted: 03/25/2008] [Indexed: 11/29/2022]
Abstract
The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.
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Affiliation(s)
- Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreienplein 10, 6703 HB Wageningen, Netherlands.
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Mizutani H, Kunishima N. Purification, crystallization and preliminary X-ray analysis of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:792-4. [PMID: 17768357 PMCID: PMC2376325 DOI: 10.1107/s1744309107039590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 08/10/2007] [Indexed: 11/10/2022]
Abstract
Fumarylacetoacetase catalyzes the final step of tyrosine and phenylalanine catabolism. A recombinant form of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8 has been crystallized by the oil-microbatch method using sodium chloride as a precipitating agent. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 93.3, b = 73.4, c = 122.6 A, beta = 111.8 degrees. The crystals are most likely to contain two dimers in the asymmetric unit, with a V(M) value of 3.32 A3 Da(-1). Diffraction data were collected at 2.2 A resolution using synchrotron radiation at beamline BL26B1 of SPring-8, Japan.
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Affiliation(s)
- Hisashi Mizutani
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cyo, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoki Kunishima
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cyo, Sayo-gun, Hyogo 679-5148, Japan
- Correspondence e-mail:
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20
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Izumi A, Rea D, Adachi T, Unzai S, Park SY, Roper DI, Tame JRH. Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli. J Mol Biol 2007; 370:899-911. [PMID: 17559873 DOI: 10.1016/j.jmb.2007.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 05/01/2007] [Accepted: 05/03/2007] [Indexed: 10/23/2022]
Abstract
HpcG catalyses the hydration of a carbon-carbon double bond without the aid of any cofactor other than a simple divalent metal ion such as Mg(2+). Since the substrate has a nearby carbonyl group, it is believed that it first isomerises to form a pair of conjugated double bonds in the enol tautomer before Michael addition of water. Previous chemical studies of the reaction, and that of the related enzyme MhpD, have failed to provide a clear picture of the mechanism. The substrate itself is unstable, preventing co-crystallisation or soaking of crystals, but oxalate is a strong competitive inhibitor. We have solved the crystal structure of the protein in the apo form, and with magnesium and oxalate bound. Modelling substrate into the active site suggests the attacking water molecule is not part of the metal coordination shell, in contrast to a previous proposal. Our model suggests that geometrically strained cis isomer intermediates do not lie on the reaction pathway, and that separate groups are involved in the isomerisation and hydration steps.
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Affiliation(s)
- Atsushi Izumi
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan
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21
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Dixon DP, Edwards R. Enzymes of tyrosine catabolism in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2006; 171:360-6. [PMID: 22980205 DOI: 10.1016/j.plantsci.2006.04.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 04/12/2006] [Accepted: 04/13/2006] [Indexed: 05/24/2023]
Abstract
Tyrosine catabolism is an essential pathway in animals, but its role in plants is unclear. The first steps of tyrosine degradation lead to the formation of homogentisate. In animals this is then sequentially acted on by homogentisate dioxygenase (HGO), maleylacetoacetate isomerase (MAAI) and fumarylacetoacetate hydrolase (FAH) to generate fumarate and acetoacetate. In plants, homogentisate is used to generate the essential redox metabolites tocopherol and plastoquinone, which effectively act as an alternative metabolic fate for tyrosine. Having determined that a zeta class glutathione transferase from Arabidopsis thaliana is a functional MAAI, we have looked for evidence that the mammalian degradation pathway could also operate in plants. Based on array and quantitative PCR experiments, the A. thaliana homologues AtHGO, AtMAAI and AtFAH could be shown to be expressed, with AtHGO and AtMAAI showing evidence of co-regulation. cDNAs encoding AtHGO, AtMAAI and AtFAH were cloned in Escherichia coli and shown to represent a fully functional catabolic pathway when combined in vitro. The significance of this pathway, including increased transcription of the associated enzymes in senescing tissue, compartmentalisation and impact on flux into synthesis of Vitamin E and other tocopherols of biotechnological interest is discussed.
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Affiliation(s)
- David P Dixon
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
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Chevallet M, Lescuyer P, Diemer H, van Dorsselaer A, Leize-Wagner E, Rabilloud T. Alterations of the mitochondrial proteome caused by the absence of mitochondrial DNA: A proteomic view. Electrophoresis 2006; 27:1574-83. [PMID: 16548050 PMCID: PMC2797067 DOI: 10.1002/elps.200500704] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the mitochondrial rRNAs and a few tRNAs, we performed a comparative study on the 143B cell line and on its Rho-0 counterpart, i.e., devoid of mitochondrial DNA. Quantitative differences were found, of course in the respiratory complexes subunits, but also in the mitochondrial translation apparatus, mainly mitochondrial ribosomal proteins, and in the ion and protein import system, i.e., including membrane proteins. Various mitochondrial metabolic processes were also altered, especially electron transfer proteins and some dehydrogenases, but quite often on a few proteins for each pathway. This study also showed variations in some hypothetical or poorly characterized proteins, suggesting a mitochondrial localization for these proteins. Examples include a stomatin-like protein and a protein sharing homologies with bacterial proteins implicated in tyrosine catabolism. Proteins involved in apoptosis control are also found modulated in Rho-0 mitochondria.
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Affiliation(s)
- Mireille Chevallet
- Contrôle moléculaire de la réponse immune specifique
INSERM : U548CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble IFR
| | - Pierre Lescuyer
- Contrôle moléculaire de la réponse immune specifique
INSERM : U548CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble IFR
| | - Hélène Diemer
- Electrochimie et physicochimie des complexes et systèmes interfaciaux
CNRS : UMR7512Université Louis Pasteur - Strasbourg IG. RITZLER Institut le Bel 4, Rue Blaise Pascal 67008 STRASBOURG CEDEX,FR
| | - Alain van Dorsselaer
- Electrochimie et physicochimie des complexes et systèmes interfaciaux
CNRS : UMR7512Université Louis Pasteur - Strasbourg IG. RITZLER Institut le Bel 4, Rue Blaise Pascal 67008 STRASBOURG CEDEX,FR
| | - Emmanuelle Leize-Wagner
- Electrochimie et physicochimie des complexes et systèmes interfaciaux
CNRS : UMR7512Université Louis Pasteur - Strasbourg IG. RITZLER Institut le Bel 4, Rue Blaise Pascal 67008 STRASBOURG CEDEX,FR
| | - Thierry Rabilloud
- Contrôle moléculaire de la réponse immune specifique
INSERM : U548CEA : DSV/IRTSVUniversité Joseph Fourier - Grenoble IFR
- * Correspondence should be adressed to: Thierry Rabilloud
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Manjasetty BA, Niesen FH, Scheich C, Roske Y, Goetz F, Behlke J, Sievert V, Heinemann U, Büssow K. X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1). BMC STRUCTURAL BIOLOGY 2005; 5:21. [PMID: 16354304 PMCID: PMC1352370 DOI: 10.1186/1472-6807-5-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Accepted: 12/14/2005] [Indexed: 11/26/2022]
Abstract
Background Human Aortic Preferentially Expressed Protein-1 (APEG-1) is a novel specific smooth muscle differentiation marker thought to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs). Results Good quality crystals that were suitable for X-ray crystallographic studies were obtained following the truncation of the 14 N-terminal amino acids of APEG-1, a region predicted to be disordered. The truncated protein (termed ΔAPEG-1) consists of a single immunoglobulin (Ig) like domain which includes an Arg-Gly-Asp (RGD) adhesion recognition motif. The RGD motif is crucial for the interaction of extracellular proteins and plays a role in cell adhesion. The X-ray structure of ΔAPEG-1 was determined and was refined to sub-atomic resolution (0.96 Å). This is the best resolution for an immunoglobulin domain structure so far. The structure adopts a Greek-key β-sandwich fold and belongs to the I (intermediate) set of the immunoglobulin superfamily. The residues lying between the β-sheets form a hydrophobic core. The RGD motif folds into a 310 helix that is involved in the formation of a homodimer in the crystal which is mainly stabilized by salt bridges. Analytical ultracentrifugation studies revealed a moderate dissociation constant of 20 μM at physiological ionic strength, suggesting that APEG-1 dimerisation is only transient in the cell. The binding constant is strongly dependent on ionic strength. Conclusion Our data suggests that the RGD motif might play a role not only in the adhesion of extracellular proteins but also in intracellular protein-protein interactions. However, it remains to be established whether the rather weak dimerisation of APEG-1 involving this motif is physiogically relevant.
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Affiliation(s)
- Babu A Manjasetty
- Protein Structure Factory, c/o BESSY GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Case Centre for Proteomics, Case Western Reserve University, Upton, New York 11973, USA
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Charité Universitätsmedizin Berlin, Institut für Medizinische Physik & Biophysik, Ziegelstr. 5-9, 10098 Berlin, Germany
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, OX3 7LD, UK
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Frank Goetz
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
| | - Joachim Behlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
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24
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Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Microb Cell Fact 2005; 4:21. [PMID: 15998469 PMCID: PMC1250228 DOI: 10.1186/1475-2859-4-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/05/2005] [Indexed: 11/12/2022] Open
Abstract
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics initiative, targets human proteins for structure determination. It has implemented high throughput procedures for all steps from cloning to structure calculation. This article describes the selection of human target proteins for structure analysis, our high throughput cloning strategy, and the expression of human proteins in Escherichia coli host cells. Results and Conclusion Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
- DIFE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Jörg Schultz
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Bernd Simon
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Peer Bork
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
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