1
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Pampalone G, Chiasserini D, Pierigè F, Camaioni E, Orvietani PL, Bregalda A, Menotta M, Bellezza I, Rossi L, Cellini B, Magnani M. Biochemical Studies on Human Ornithine Aminotransferase Support a Cell-Based Enzyme Replacement Therapy in the Gyrate Atrophy of the Choroid and Retina. Int J Mol Sci 2024; 25:7931. [PMID: 39063173 DOI: 10.3390/ijms25147931] [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: 05/24/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The gyrate atrophy of the choroid and retina (GACR) is a rare genetic disease for which no definitive cure is available. GACR is due to the deficit of ornithine aminotransferase (hOAT), a pyridoxal 5'-phosphate-dependent enzyme responsible for ornithine catabolism. The hallmark of the disease is plasmatic ornithine accumulation, which damages retinal epithelium leading to progressive vision loss and blindness within the fifth decade. Here, we characterized the biochemical properties of tetrameric and dimeric hOAT and evaluated hOAT loaded in red blood cells (RBCs) as a possible enzyme replacement therapy (ERT) for GACR. Our results show that (i) hOAT has a relatively wide specificity for amino acceptors, with pyruvate being the most suitable candidate for ornithine catabolism within RBCs; (ii) both the tetrameric and dimeric enzyme can be loaded in RBC retaining their activity; and (iii) hOAT displays reduced stability in plasma, but is partly protected from inactivation upon incubation in a mixture mimicking the intracellular erythrocyte environment. Preliminary ex vivo experiments indicate that hOAT-loaded RBCs are able to metabolize extracellular ornithine at a concentration mimicking that found in patients, both in buffer and, although with lower efficiency, in plasma. Overall, our data provide a proof of concept that an RBC-mediated ERT is feasible and can be exploited as a new therapeutic approach in GACR.
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Affiliation(s)
- Gioena Pampalone
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Davide Chiasserini
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Francesca Pierigè
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy
| | - Pier Luigi Orvietani
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Alessandro Bregalda
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Ilaria Bellezza
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Luigia Rossi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
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2
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Lykins J, Moschitto MJ, Zhou Y, Filippova EV, Le HV, Tomita T, Fox BA, Bzik DJ, Su C, Rajagopala SV, Flores K, Spano F, Woods S, Roberts CW, Hua C, El Bissati K, Wheeler KM, Dovgin S, Muench SP, McPhillie M, Fishwick CW, Anderson WF, Lee PJ, Hickman M, Weiss LM, Dubey JP, Lorenzi HA, Silverman RB, McLeod RL. From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma. iScience 2024; 27:108477. [PMID: 38205261 PMCID: PMC10776954 DOI: 10.1016/j.isci.2023.108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/28/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024] Open
Abstract
Toxoplasma gondii causes morbidity, mortality, and disseminates widely via cat sexual stages. Here, we find T. gondii ornithine aminotransferase (OAT) is conserved across phyla. We solve TgO/GABA-AT structures with bound inactivators at 1.55 Å and identify an inactivator selective for TgO/GABA-AT over human OAT and GABA-AT. However, abrogating TgO/GABA-AT genetically does not diminish replication, virulence, cyst-formation, or eliminate cat's oocyst shedding. Increased sporozoite/merozoite TgO/GABA-AT expression led to our study of a mutagenized clone with oocyst formation blocked, arresting after forming male and female gametes, with "Rosetta stone"-like mutations in genes expressed in merozoites. Mutations are similar to those in organisms from plants to mammals, causing defects in conception and zygote formation, affecting merozoite capacitation, pH/ionicity/sodium-GABA concentrations, drawing attention to cyclic AMP/PKA, and genes enhancing energy or substrate formation in TgO/GABA-AT-related-pathways. These candidates potentially influence merozoite's capacity to make gametes that fuse to become zygotes, thereby contaminating environments and causing disease.
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Affiliation(s)
- Joseph Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew J. Moschitto
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hoang V. Le
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Tadakimi Tomita
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A. Fox
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J. Bzik
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Seesandra V. Rajagopala
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kristin Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Furio Spano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Cong Hua
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kelsey M. Wheeler
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah Dovgin
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, The University of Leeds, Leeds, West York LS2 9JT, UK
| | - Martin McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Colin W.G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Patricia J. Lee
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Mark Hickman
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Louis M. Weiss
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jitender P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hernan A. Lorenzi
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Rima L. McLeod
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL 60637, USA
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3
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Silverman RB. Inactivators of Ornithine Aminotransferase for the Treatment of Hepatocellular Carcinoma. ACS Med Chem Lett 2021; 13:38-49. [PMID: 35059122 PMCID: PMC8762738 DOI: 10.1021/acsmedchemlett.1c00526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/22/2021] [Indexed: 01/16/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the second or third leading cause of cancer mortality worldwide (depending on which statistics are used), yet there is no effective treatment. Currently, there are nine FDA-approved drugs for HCC, five monoclonal antibodies and four tyrosine kinase inhibitors. Ornithine aminotransferase (OAT) has been validated as a target in preclinical studies, which demonstrates that it is a potential target to treat HCC. Currently, there are no OAT inactivators in clinical trials for HCC. This Innovation describes evidence to support inhibition of OAT as a novel approach for HCC tumor growth inhibition. After the mechanism of OAT is discussed, the origins of our involvement in OAT inactivation, based on our previous work on mechanism-based inactivation of GABA-AT, are described. Once it was demonstrated that OAT inactivation does lead to HCC tumor growth inhibition, new selective OAT inactivators were designed and their inactivation mechanisms were elucidated. A summary of these mechanistic studies is presented. Inactivators of OAT provide the potential for treatment of HCC, targeting the Wnt/β-catenin pathway.
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4
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Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB. Turnover and Inactivation Mechanisms for ( S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8689-8703. [PMID: 34097381 PMCID: PMC8367020 DOI: 10.1021/jacs.1c02456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inhibition of human ornithine δ-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
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Affiliation(s)
- Sida Shen
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Mauricio T. Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Glaucio M. Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Neil L. Kelleher
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois, 60611, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
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5
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Zhu W, Doubleday PF, Butrin A, Weerawarna PM, Melani R, Catlin DS, Dwight TA, Liu D, Kelleher NL, Silverman RB. Remarkable and Unexpected Mechanism for ( S)-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8193-8207. [PMID: 34014654 PMCID: PMC8369387 DOI: 10.1021/jacs.1c03572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that was recently found to play an important role in the metabolic reprogramming of hepatocellular carcinoma (HCC) via the proline and glutamine metabolic pathways. The selective inhibition of hOAT by compound 10 exhibited potent in vivo antitumor activity. Inspired by the discovery of the aminotransferase inactivator (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid (5), we rationally designed, synthesized, and evaluated a series of six-membered-ring analogs. Among them, 14 was identified as a new selective hOAT inactivator, which demonstrated a potency 22× greater than that of 10. Three different types of protein mass spectrometry approaches and two crystallographic approaches were employed to identify the structure of hOAT-14 and the formation of a remarkable final adduct (32') in the active site. These spectral studies reveal an enzyme complex heretofore not observed in a PLP-dependent enzyme, which has covalent bonds to two nearby residues. Crystal soaking experiments and molecular dynamics simulations were carried out to identify the structure of the active-site intermediate 27' and elucidate the order of the two covalent bonds that formed, leading to 32'. The initial covalent reaction of the activated warhead occurs with *Thr322 from the second subunit, followed by a subsequent nucleophilic attack by the catalytic residue Lys292. The turnover mechanism of 14 by hOAT was supported by a mass spectrometric analysis of metabolites and fluoride ion release experiments. This novel mechanism for hOAT with 14 will contribute to the further rational design of selective inactivators and an understanding of potential inactivation mechanisms by aminotransferases.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Pathum M. Weerawarna
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel S. Catlin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Timothy A. Dwight
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Neil L. Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois 60611, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
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6
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Butrin A, Beaupre BA, Kadamandla N, Zhao P, Shen S, Silverman RB, Moran GR, Liu D. Structural and Kinetic Analyses Reveal the Dual Inhibition Modes of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic Acid (BCF 3). ACS Chem Biol 2021; 16:67-75. [PMID: 33316155 PMCID: PMC8474141 DOI: 10.1021/acschembio.0c00728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common form of liver cancer and the leading cause of death among people with cirrhosis. HCC is typically diagnosed in advanced stages when tumors are resistant to both radio- and chemotherapy. Human ornithine aminotransferase (hOAT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme involved in glutamine and proline metabolism. Because hOAT is overexpressed in HCC cells and a contributing factor for the uncontrolled cellular division that propagates malignant tumors (Ueno et al. J. Hepatol. 2014, 61, 1080-1087), it is a potential drug target for the treatment of HCC. (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid (BCF3) has been shown in animal models to slow the progression of HCC by acting as a selective and potent mechanism-based inactivator of OAT (Zigmond et al. ACS Med. Chem. Lett. 2015, 6, 840-844). Previous studies have shown that the BCF3-hOAT reaction has a bifurcation in which only 8% of the inhibitor inactivates the enzyme while the remaining 92% ultimately acts as a substrate and undergoes hydrolysis to regenerate the active PLP form of the enzyme. In this manuscript, the rate-limiting step of the inactivation mechanism was determined by stopped-flow spectrophotometry and time-dependent 19F NMR experiments to be the decay of a long-lived external aldimine species. A crystal structure of this transient complex revealed both the structural basis for fractional irreversible inhibition and the principal mode of inhibition of hOAT by BCF3, which is to trap the enzyme in this transient but quasi-stable external aldimine form.
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Affiliation(s)
- Arseniy Butrin
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Noel Kadamandla
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Peidong Zhao
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Sida Shen
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Richard B. Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Dali Liu
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660.,Corresponding author; phone: (773)508-3093;
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7
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Montioli R, Bellezza I, Desbats MA, Borri Voltattorni C, Salviati L, Cellini B. Deficit of human ornithine aminotransferase in gyrate atrophy: Molecular, cellular, and clinical aspects. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140555. [PMID: 33068755 DOI: 10.1016/j.bbapap.2020.140555] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Gyrate Atrophy (GA) of the choroid and retina (MIM# 258870) is an autosomal recessive disorder due to mutations of the OAT gene encoding ornithine-delta-aminotransferase (OAT), associated with progressive retinal deterioration and blindness. The disease has a theoretical global incidence of approximately 1:1,500,000. OAT is mainly involved in ornithine catabolism in adults, thus explaining the hyperornithinemia as hallmark of the disease. Patients are treated with an arginine-restricted diet, to limit ornithine load, or the administration of Vitamin B6, a precursor of the OAT coenzyme pyridoxal phosphate. Although the clinical and genetic aspects of GA are known for many years, the enzymatic phenotype of pathogenic variants and their response to Vitamin B6, as well as the molecular mechanisms explaining retinal damage, are poorly clarified. Herein, we provide an overview of the current knowledge on the biochemical properties of human OAT and on the molecular, cellular, and clinical aspects of GA.
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Affiliation(s)
- Riccardo Montioli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Ilaria Bellezza
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Perugia, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Carla Borri Voltattorni
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Perugia, Italy.
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8
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Moschitto MJ, Doubleday PF, Catlin DS, Kelleher NL, Liu D, Silverman RB. Mechanism of Inactivation of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid. J Am Chem Soc 2019; 141:10711-10721. [PMID: 31251613 DOI: 10.1021/jacs.9b03254] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The inhibition of ornithine aminotransferase (OAT), a pyridoxal 5'-phosphate-dependent enzyme, has been implicated as a treatment for hepatocellular carcinoma (HCC), the most common form of liver cancer, for which there is no effective treatment. From a previous evaluation of our aminotransferase inhibitors, (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride (1) was found to be a selective and potent inactivator of human OAT (hOAT), which inhibited the growth of HCC in athymic mice implanted with human-derived HCC, even at a dose of 0.1 mg/kg. Currently, investigational new drug (IND)-enabling studies with 1 are underway. The inactivation mechanism of 1, however, has proved to be elusive. Here we propose three possible mechanisms, based on mechanisms of known aminotransferase inactivators: Michael addition, enamine addition, and fluoride ion elimination followed by conjugate addition. On the basis of crystallography and intact protein mass spectrometry, it was determined that 1 inactivates hOAT through fluoride ion elimination to an activated 1,1'-difluoroolefin, followed by conjugate addition and hydrolysis. This result was confirmed with additional studies, including the detection of the cofactor structure by mass spectrometry and through the identification of turnover metabolites. On the basis of this inactivation mechanism and to provide further evidence for the mechanism, analogues of 1 (19, 20) were designed, synthesized, and demonstrated to have the predicted selective inactivation mechanism. These analogues highlight the importance of the trifluoromethyl group and provide a basis for future inactivator design.
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Affiliation(s)
| | | | - Daniel S Catlin
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | | | - Dali Liu
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
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9
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Lykins JD, Filippova EV, Halavaty AS, Minasov G, Zhou Y, Dubrovska I, Flores KJ, Shuvalova LA, Ruan J, El Bissati K, Dovgin S, Roberts CW, Woods S, Moulton JD, Moulton H, McPhillie MJ, Muench SP, Fishwick CWG, Sabini E, Shanmugam D, Roos DS, McLeod R, Anderson WF, Ngô HM. CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii. Front Cell Infect Microbiol 2018; 8:352. [PMID: 30345257 PMCID: PMC6182094 DOI: 10.3389/fcimb.2018.00352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Toxoplasma gondii, an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.
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Affiliation(s)
- Joseph D. Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Andrei S. Halavaty
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Ievgeniia Dubrovska
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kristin J. Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ludmilla A. Shuvalova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
| | - Sarah Dovgin
- Illinois Math and Science Academy, Aurora, IL, United States
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - Hong Moulton
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Martin J. McPhillie
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Colin W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Elisabetta Sabini
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - David S. Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL, United States
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL, United States
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- BrainMicro LLC, New Haven, CT, United States
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10
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Montioli R, Zamparelli C, Borri Voltattorni C, Cellini B. Oligomeric State and Thermal Stability of Apo- and Holo- Human Ornithine δ-Aminotransferase. Protein J 2017; 36:174-185. [PMID: 28345116 PMCID: PMC5432616 DOI: 10.1007/s10930-017-9710-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human ornithine δ-aminotransferase (hOAT) (EC 2.6.1.13) is a mitochondrial pyridoxal 5′-phosphate (PLP)-dependent aminotransferase whose deficit is associated with gyrate atrophy, a rare autosomal recessive disorder causing progressive blindness and chorioretinal degeneration. Here, both the apo- and holo-form of recombinant hOAT were characterized by means of spectroscopic, kinetic, chromatographic and computational techniques. The results indicate that apo and holo-hOAT (a) show a similar tertiary structure, even if apo displays a more pronounced exposure of hydrophobic patches, (b) exhibit a tetrameric structure with a tetramer-dimer equilibrium dissociation constant about fivefold higher for the apoform with respect to the holoform, and (c) have apparent Tm values of 46 and 67 °C, respectively. Moreover, unlike holo-hOAT, apo-hOAT is prone to unfolding and aggregation under physiological conditions. We also identified Arg217 as an important hot-spot at the dimer–dimer interface of hOAT and demonstrated that the artificial dimeric variant R217A exhibits spectroscopic properties, Tm values and catalytic features similar to those of the tetrameric species. This finding indicates that the catalytic unit of hOAT is the dimer. However, under physiological conditions the apo-tetramer is slightly less prone to unfolding and aggregation than the apo-dimer. The possible implications of the data for the intracellular stability and regulation of hOAT are discussed.
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Affiliation(s)
- Riccardo Montioli
- Department of Neuroscience, Biomedicine and Movement Sciences (Section of Biological Chemistry), University of Verona, Strada Le Grazie 8, 37134, Verona, Italy.
| | | | - Carla Borri Voltattorni
- Department of Neuroscience, Biomedicine and Movement Sciences (Section of Biological Chemistry), University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Barbara Cellini
- Department of Neuroscience, Biomedicine and Movement Sciences (Section of Biological Chemistry), University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
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11
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Amorim Franco TM, Favrot L, Vergnolle O, Blanchard JS. Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine. ACS Chem Biol 2017; 12:1235-1244. [PMID: 28272868 DOI: 10.1021/acschembio.7b00142] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The branched-chain aminotransferase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme responsible for the final step in the biosynthesis of all three branched-chain amino acids, l-leucine, l-isoleucine, and l-valine, in bacteria. We have investigated the mechanism of inactivation of the branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) by d- and l-cycloserine. d-Cycloserine is currently used only in the treatment of multidrug-drug-resistant tuberculosis. Our results show a time- and concentration-dependent inactivation of MtIlvE by both isomers, with l-cycloserine being a 40-fold better inhibitor of the enzyme. Minimum inhibitory concentration (MIC) studies revealed that l-cycloserine is a 10-fold better inhibitor of Mycobacterium tuberculosis growth than d-cycloserine. In addition, we have crystallized the MtIlvE-d-cycloserine inhibited enzyme, determining the structure to 1.7 Å. The structure of the covalent d-cycloserine-PMP adduct bound to MtIlvE reveals that the d-cycloserine ring is planar and aromatic, as previously observed for other enzyme systems. Mass spectrometry reveals that both the d-cycloserine- and l-cycloserine-PMP complexes have the same mass, and are likely to be the same aromatized, isoxazole product. However, the kinetics of formation of the MtIlvE d-cycloserine-PMP and MtIlvE l-cycloserine-PMP adducts are quite different. While the kinetics of the formation of the MtIlvE d-cycloserine-PMP complex can be fit to a single exponential, the formation of the MtIlvE l-cycloserine-PMP complex occurs in two steps. We propose a chemical mechanism for the inactivation of d- and l-cycloserine which suggests a stereochemically determined structural role for the differing kinetics of inactivation. These results demonstrate that the mechanism of action of d-cycloserine's activity against M. tuberculosis may be more complicated than previously thought and that d-cycloserine may compromise the in vivo activity of multiple PLP-dependent enzymes, including MtIlvE.
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Affiliation(s)
- Tathyana Mar Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Lorenza Favrot
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John S. Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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12
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Ginguay A, Cynober L, Curis E, Nicolis I. Ornithine Aminotransferase, an Important Glutamate-Metabolizing Enzyme at the Crossroads of Multiple Metabolic Pathways. BIOLOGY 2017; 6:biology6010018. [PMID: 28272331 PMCID: PMC5372011 DOI: 10.3390/biology6010018] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023]
Abstract
Ornithine δ-aminotransferase (OAT, E.C. 2.6.1.13) catalyzes the transfer of the δ-amino group from ornithine (Orn) to α-ketoglutarate (aKG), yielding glutamate-5-semialdehyde and glutamate (Glu), and vice versa. In mammals, OAT is a mitochondrial enzyme, mainly located in the liver, intestine, brain, and kidney. In general, OAT serves to form glutamate from ornithine, with the notable exception of the intestine, where citrulline (Cit) or arginine (Arg) are end products. Its main function is to control the production of signaling molecules and mediators, such as Glu itself, Cit, GABA, and aliphatic polyamines. It is also involved in proline (Pro) synthesis. Deficiency in OAT causes gyrate atrophy, a rare but serious inherited disease, a further measure of the importance of this enzyme.
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Affiliation(s)
- Antonin Ginguay
- Clinical Chemistry, Cochin Hospital, GH HUPC, AP-HP, 75014 Paris, France.
- Laboratory of Biological Nutrition, EA 4466 PRETRAM, Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France.
| | - Luc Cynober
- Clinical Chemistry, Cochin Hospital, GH HUPC, AP-HP, 75014 Paris, France.
- Laboratory of Biological Nutrition, EA 4466 PRETRAM, Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France.
| | - Emmanuel Curis
- Laboratoire de biomathématiques, plateau iB², Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France.
- UMR 1144, INSERM, Université Paris Descartes, 75006 Paris, France.
- UMR 1144, Université Paris Descartes, 75006 Paris, France.
- Service de biostatistiques et d'informatique médicales, hôpital Saint-Louis, Assistance publique-hôpitaux de Paris, 75010 Paris, France.
| | - Ioannis Nicolis
- Laboratoire de biomathématiques, plateau iB², Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France.
- EA 4064 "Épidémiologie environnementale: Impact sanitaire des pollutions", Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France.
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13
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Sivashanmugam M, J J, V U, K N S. Ornithine and its role in metabolic diseases: An appraisal. Biomed Pharmacother 2016; 86:185-194. [PMID: 27978498 DOI: 10.1016/j.biopha.2016.12.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/16/2016] [Accepted: 12/04/2016] [Indexed: 11/28/2022] Open
Abstract
Ornithine is a non-essential amino acid produced as an intermediate molecule in urea cycle. It is a key substrate for the synthesis of proline, polyamines and citrulline. Ornithine also plays an important role in the regulation of several metabolic processes leading to diseases like hyperorithinemia, hyperammonemia, gyrate atrophy and cancer in humans. However, the mechanism of action behind the multi-faceted roles of ornithine is yet to be unraveled completely. Several types of cancers are also characterized by excessive polyamine synthesis from ornithine by different rate limiting enzymes. Hence, in this review we aim to provide extensive insights on potential roles of ornithine in many of the disease related cellular processes and also on the structural features of ornithine interacting proteins, enabling development of therapeutic modalities.
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Affiliation(s)
- Muthukumaran Sivashanmugam
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India; School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Jaidev J
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India
| | - Umashankar V
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
| | - Sulochana K N
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
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14
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Amorim Franco TM, Hegde S, Blanchard JS. Chemical Mechanism of the Branched-Chain Aminotransferase IlvE from Mycobacterium tuberculosis. Biochemistry 2016; 55:6295-6303. [PMID: 27780341 DOI: 10.1021/acs.biochem.6b00928] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The biosynthetic pathway of the branched-chain amino acids is essential for Mycobacterium tuberculosis growth and survival. We report here the kinetic and chemical mechanism of the pyridoxal 5'-phosphate (PLP)-dependent branched-chain aminotransferase, IlvE, from M. tuberculosis (MtIlvE). This enzyme is responsible for the final step of the synthesis of the branched-chain amino acids isoleucine, leucine, and valine. As seen in other aminotransferases, MtIlvE displays a ping-pong kinetic mechanism. pK values were identified from the pH dependence on V as well as V/K, indicating that the phosphate ester of the PLP cofactor, and the α-amino group from l-glutamate and the active site Lys204, play roles in acid-base catalysis and binding, respectively. An intrinsic primary kinetic isotope effect was identified for the α-C-H bond cleavage of l-glutamate. Large solvent kinetic isotope effect values for the ping and pong half-reactions were also identified. The absence of a quininoid intermediate in combination with the Dkobs in our multiple kinetic isotope effects under single-turnover conditions suggests a concerted type of mechanism. The deprotonation of C2 of l-glutamate and the protonation of C4' of the PLP cofactor happen synchronously in the ping half-reaction. A chemical mechanism is proposed on the basis of the results obtained here.
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Affiliation(s)
- Tathyana M Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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15
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Zigmond E, Ya’acov AB, Lee H, Lichtenstein Y, Shalev Z, Smith Y, Zolotarov L, Ziv E, Kalman R, Le HV, Lu H, Silverman RB, Ilan Y. Suppression of Hepatocellular Carcinoma by Inhibition of Overexpressed Ornithine Aminotransferase. ACS Med Chem Lett 2015; 6:840-4. [PMID: 26288681 DOI: 10.1021/acsmedchemlett.5b00153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 05/29/2015] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma is the second leading cause of cancer death worldwide. DNA microarray analysis identified the ornithine aminotransferase (OAT) gene as a prominent gene overexpressed in hepatocellular carcinoma (HCC) from Psammomys obesus. In vitro studies demonstrated inactivation of OAT by gabaculine (1), a neurotoxic natural product, which suppressed in vitro proliferation of two HCC cell lines. Alpha-fetoprotein (AFP) secretion, a biomarker for HCC, was suppressed by gabaculine in both cell lines, but not significantly. Because of the active site similarity between GABA aminotransferase (GABA-AT) and OAT, a library of 24 GABA-AT inhibitors was screened to identify a more selective inhibitor of OAT. (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidene)cyclopentane-1-carboxylic acid (2) was found to be an inactivator of OAT that only weakly inhibits GABA-AT, l-aspartate aminotransferase, and l-alanine aminotransferase. In vitro administration of 2 significantly suppressed AFP secretion in both Hep3B and HepG2 HCC cells; in vivo, 2 significantly suppressed AFP serum levels and tumor growth in HCC-harboring mice, even at 0.1 mg/kg. Overexpression of the OAT gene in HCC and the ability to block the growth of HCC by OAT inhibitors support the role of OAT as a potential therapeutic target to inhibit HCC growth. This is the first demonstration of suppression of HCC by an OAT inactivator.
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Affiliation(s)
| | | | - Hyunbeom Lee
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | | | | | | | | | - Hoang V. Le
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Hejun Lu
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Department of Chemistry,
Department of Molecular Biosciences, Chemistry of Life Processes Institute,
and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
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16
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Lee H, Juncosa JI, Silverman RB. Ornithine aminotransferase versus GABA aminotransferase: implications for the design of new anticancer drugs. Med Res Rev 2014; 35:286-305. [PMID: 25145640 DOI: 10.1002/med.21328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ornithine aminotransferase (OAT) and γ-aminobutyric acid aminotransferase (GABA-AT) are classified under the same evolutionary subgroup and share a large portion of structural, functional, and mechanistic features. Therefore, it is not surprising that many molecules that bind to GABA-AT also bind well to OAT. Unlike GABA-AT, OAT had not been viewed as a potential therapeutic target until recently; consequently, the number of therapeutically viable molecules that target OAT is very limited. In this review the two enzymes are compared with respect to their active-site structures, catalytic and inactivation mechanisms, and selective inhibitors. Insight is offered that could aid in the design and development of new selective inhibitors of OAT for the treatment of cancer.
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Affiliation(s)
- Hyunbeom Lee
- Center for Molecular Innovation and Drug Discovery, Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
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17
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Pryor EE, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. Structure of the integral membrane protein CAAX protease Ste24p. Science 2013; 339:1600-4. [PMID: 23539602 DOI: 10.1126/science.1232048] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.
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18
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Sayer C, Isupov MN, Westlake A, Littlechild JA. Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:564-76. [PMID: 23519665 PMCID: PMC3606037 DOI: 10.1107/s0907444912051670] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/21/2012] [Indexed: 11/10/2022]
Abstract
The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases.
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Affiliation(s)
- Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Aaron Westlake
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
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19
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Sayer C, Bommer M, Isupov M, Ward J, Littlechild J. Crystal structure and substrate specificity of the thermophilic serine:pyruvate aminotransferase fromSulfolobus solfataricus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:763-72. [DOI: 10.1107/s0907444912011274] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/14/2012] [Indexed: 11/10/2022]
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20
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Liu D, Pozharski E, Fu M, Silverman RB, Ringe D. Mechanism of inactivation of Escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid . Biochemistry 2010; 49:10507-15. [PMID: 21033689 PMCID: PMC3013228 DOI: 10.1021/bi101325z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a potential drug to treat neurological diseases, the mechanism-based inhibitor (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) has been found to inhibit the γ-aminobutyric acid aminotransferase (GABA-AT) reaction. To circumvent the difficulties in structural studies of a S-ADFA-enzyme complex using GABA-AT, l-aspartate aminotransferase (l-AspAT) from Escherichia coli was used as a model PLP-dependent enzyme. Crystal structures of the E. coli aspartate aminotransferase with S-ADFA bound to the active site were obtained via cocrystallization at pH 7.5 and 8. The complex structures suggest that S-ADFA inhibits the transamination reaction by forming adducts with the catalytic lysine 246 via a covalent bond while producing 1 equiv of pyridoxamine 5'-phosphate (PMP). Based on the structures, formation of the K246-S-ADFA adducts requires a specific initial binding configuration of S-ADFA in the l-AspAT active site, as well as deprotonation of the ε-amino group of lysine 246 after the formation of the quinonoid and/or ketimine intermediate in the overall inactivation reaction.
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Affiliation(s)
- Dali Liu
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Edwin Pozharski
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Mengmeng Fu
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Dagmar Ringe
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
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Dey S, Lane JM, Lee RE, Rubin EJ, Sacchettini JC. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Biochemistry 2010; 49:6746-60. [PMID: 20565114 DOI: 10.1021/bi902097j] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analogue sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.
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Affiliation(s)
- Sanghamitra Dey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
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Stránská J, Tylichová M, Kopecný D, Snégaroff J, Sebela M. Biochemical characterization of pea ornithine-delta-aminotransferase: substrate specificity and inhibition by di- and polyamines. Biochimie 2010; 92:940-8. [PMID: 20381578 DOI: 10.1016/j.biochi.2010.03.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/30/2010] [Indexed: 11/20/2022]
Abstract
Ornithine-delta-aminotransferase (OAT, EC 2.6.1.13) catalyzes the transamination of L-ornithine to L-glutamate-gamma-semialdehyde. The physiological role of OAT in plants is not yet well understood. It is probably related to arginine catabolism resulting in glutamate but the enzyme has also been associated with stress-induced proline biosynthesis. We investigated the enzyme from pea (PsOAT) to assess whether diamines and polyamines may serve as substrates or they show inhibitory properties. First, a cDNA coding for PsOAT was cloned and expressed in Escherichia coli to obtain a recombinant protein with a C-terminal 6xHis tag. Recombinant PsOAT was purified under native conditions by immobilized metal affinity chromatography and its molecular and kinetic properties were characterized. Protein identity was confirmed by peptide mass fingerprinting after proteolytic digestion. The purified PsOAT existed as a monomer of 50 kDa and showed typical spectral properties of enzymes containing pyridoxal-5'-phosphate as a prosthetic group. The cofactor content of PsOAT was estimated to be 0.9 mol per mol of the monomer by a spectrophotometric analysis with phenylhydrazine. L-Ornithine was the best substrate (K(m)=15 mM) but PsOAT also slowly converted N(alpha)-acetyl-L-ornithine. In these reactions, 2-oxoglutarate was the exclusive amino group acceptor (K(m)=2mM). The enzyme had a basic optimal pH of 8.8 and displayed relatively high temperature optimum. Diamines and polyamines were not accepted as substrates. On the other hand, putrescine, spermidine and others represented weak non-competitive inhibitors. A model of the molecular structure of PsOAT was obtained using the crystal structure of human OAT as a template.
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Affiliation(s)
- Jana Stránská
- Department of Biochemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic
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23
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Jortzik E, Fritz-Wolf K, Sturm N, Hipp M, Rahlfs S, Becker K. Redox regulation of Plasmodium falciparum ornithine δ-aminotransferase. J Mol Biol 2010; 402:445-59. [PMID: 20673832 DOI: 10.1016/j.jmb.2010.07.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 07/16/2010] [Accepted: 07/20/2010] [Indexed: 11/16/2022]
Abstract
Ornithine δ-aminotransferase (OAT) of the malaria parasite Plasmodium falciparum catalyzes the reversible conversion of ornithine into glutamate-5-semialdehyde and glutamate and is-in contrast to its human counterpart-activated by thioredoxin (Trx) by a factor of 10. Trx, glutaredoxin, and plasmoredoxin are redox-active proteins that play a crucial role in the maintenance and control of redox reactions, and were shown to interact with P. falciparum OAT. OAT, which is involved in ornithine homeostasis and proline biosynthesis, is essential for mitotic cell division in rapidly growing cells, thus representing a potential target for chemotherapeutic intervention. Here we report the three-dimensional crystal structure of P. falciparum OAT at 2.3 Å resolution. The overall structure is very similar to that of the human OAT. However, in plasmodial OAT, the loop involved in substrate binding contains two cysteine residues, which are lacking in human OAT. Site-directed mutagenesis of these cysteines and functional analysis demonstrated that Cys154 and Cys163 mediate the interaction with Trx. Interestingly, the Cys154→Ser mutant has a strongly reduced specific activity, most likely due to impaired binding of ornithine. Cys154 and Cys163 are highly conserved in Plasmodium but do not exist in other organisms, suggesting that redox regulation of OAT by Trx is specific for malaria parasites. Plasmodium might require a tight Trx-mediated control of OAT activity for coordinating ornithine homeostasis, polyamine synthesis, proline synthesis, and mitotic cell division.
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Affiliation(s)
- Esther Jortzik
- Interdisciplinary Research Center, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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24
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Lepore BW, Liu D, Peng Y, Fu M, Yasuda C, Manning JM, Silverman RB, Ringe D. Chiral discrimination among aminotransferases: inactivation by 4-amino-4,5-dihydrothiophenecarboxylic acid. Biochemistry 2010; 49:3138-47. [PMID: 20192272 DOI: 10.1021/bi902052x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mechanism-based inhibitors such as cycloserine and gabaculine can inactivate aminotransferases via reactions of the compounds with the pyridoxal phosphate cofactor forming an irreversible adduct. The reaction is chirally specific in that any one enzyme usually only recognizes one enantiomer of the inactivator. For instance, l-aspartate aminotransferase (l-AspAT) is inactivated by 4-amino-4,5-dihydro-2-thiophenecarboxylic acid (ADTA), however, only by the S-isomer. We have now shown that d-amino acid aminotransferase (d-a-AT) is irreversibly inactivated by the R-isomer of the same compound. The X-ray crystal structure (PDB code: 3LQS ) of the inactivated enzyme shows that in the product the enzyme no longer makes a Schiff base linkage to the pyridoxal 5'-phosphate (PLP) cofactor, and instead the compound has formed a derivative of the cofactor. The adduct is similar to that formed between d-cycloserine and d-a-AT or alanine racemase (Ala-Rac) in that the thiophene ring of R-ADTA is intact and seems to be aromatic. The plane of the ring is rotated by nearly 90 degrees with respect to the plane of the pyridine ring of the cofactor, in comparison with the enzyme inactivated by cycloserine. Based on the structure of the product, the mechanism of inactivation most probably involves a transamination followed by aromatization to form an aromatic thiophene ring.
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Affiliation(s)
- Bryan W Lepore
- Graduate Program in Bioorganic Chemistry, Graduate Program in Biophysics and Biochemistry, Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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25
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A Common Structural Basis for pH- and Calmodulin-mediated Regulation in Plant Glutamate Decarboxylase. J Mol Biol 2009; 392:334-51. [DOI: 10.1016/j.jmb.2009.06.080] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/27/2009] [Accepted: 06/29/2009] [Indexed: 01/11/2023]
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Stránská J, Kopecný D, Tylichová M, Snégaroff J, Sebela M. Ornithine delta-aminotransferase: An enzyme implicated in salt tolerance in higher plants. PLANT SIGNALING & BEHAVIOR 2008; 3:929-35. [PMID: 19513195 PMCID: PMC2633738 DOI: 10.4161/psb.6771] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 08/12/2008] [Indexed: 05/08/2023]
Abstract
This review deals with biochemical and physiological aspects of plant ornithine d-aminotransferase (OAT, EC 2.6.1.13). OAT is a mitochondrial enzyme containing pyridoxal-5'-phosphate as a cofactor, which catalyzes the conversion of L-ornithine to L-glutamate gamma-semialdehyde using 2-oxoglutarate as a terminal amino group acceptor. It has been described in humans, animals, insects, plants and microorganisms. Based on the crystal structure of human OAT, both substrate binding and reaction mechanism of the enzyme are well understood. OAT shows a large structural and mechanistic similarity to other enzymes from the subgroup III of aminotransferases, which transfer an amino group from a carbon atom that does not carry a carboxyl function. In plants, the enzyme has been implicated in proline biosynthesis and accumulation (via pyrroline-5-carboxylate), which represents a way to regulate cellular osmolarity in response to osmotic stress. However, the exact metabolic pathway involving OAT remains a subject of controversy.
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Affiliation(s)
- Jana Stránská
- Department of Biochemistry; Faculty of Science; Palacký University; Olomouc Czech Republic
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27
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Abstract
The proline catabolic enzymes proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase catalyze the 4-electron oxidation of proline to glutamate. These enzymes play important roles in cellular redox control, superoxide generation, apoptosis and cancer. In some bacteria, the two enzymes are fused into the bifunctional enzyme, proline utilization A. Here we review the three-dimensional structural information that is currently available for proline catabolic enzymes. Crystal structures have been determined for bacterial monofunctional proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase, as well as the proline dehydrogenase and DNA-binding domains of proline utilization A. Some of the functional insights provided by analyses of these structures are discussed, including substrate recognition, catalytic mechanism, biochemical basis of inherited proline catabolic disorders and DNA recognition by proline utilization A.
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Rajaram V, Ratna Prasuna P, Savithri HS, Murthy MRN. Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: Studies on substrate specificity and inhibitor binding. Proteins 2007; 70:429-41. [PMID: 17680699 DOI: 10.1002/prot.21567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Acetylornithine aminotransferase (AcOAT) is one of the key enzymes involved in arginine metabolism and catalyzes the conversion of N-acetylglutamate semialdehyde to N-acetylornithine (AcOrn) in the presence of L-glutamate. It belongs to the Type I subgroup II family of pyridoxal 5'-phosphate (PLP) dependent enzymes. E. coli biosynthetic AcOAT (eAcOAT) also catalyzes the conversion of N-succinyl-L-2-amino-6-oxopimelate to N-succinyl-L,L-diaminopimelate, one of the steps in lysine biosynthesis. In view of the critical role of AcOAT in lysine and arginine biosynthesis, structural studies were initiated on the enzyme from S. typhimurium (sAcOAT). The K(m) and k(cat)/K(m) values determined with the purified sAcOAT suggested that the enzyme had much higher affinity for AcOrn than for ornithine (Orn) and was more efficient than eAcOAT. sAcOAT was inhibited by gabaculine (Gcn) with an inhibition constant (K(i)) of 7 microM and a second-order rate constant (k(2)) of 0.16 mM(-1) s(-1). sAcOAT, crystallized in the unliganded form and in the presence of Gcn or L-glutamate, diffracted to a maximum resolution of 1.90 A and contained a dimer in the asymmetric unit. The structure of unliganded sAcOAT showed significant electron density for PLP in only one of the subunits (subunit A). The asymmetry in PLP binding could be attributed to the ordering of the loop L(alphak-) (betam) in only one subunit (subunit B; the loop from subunit B comes close to the phosphate group of PLP in subunit A). Structural and spectral studies of sAcOAT with Gcn suggested that the enzyme might have a low affinity for PLP-Gcn complex. Comparison of sAcOAT with T. thermophilus AcOAT and human ornithine aminotransferase suggested that the higher specificity of sAcOAT towards AcOrn may not be due to specific changes in the active site residues but could result from minor conformational changes in some of them. This is the first structural report of AcOAT from a mesophilic organism and could serve as a basis for drug design as the enzyme is important for bacterial cell wall biosynthesis.
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Affiliation(s)
- V Rajaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Wagemaker MJM, Eastwood DC, Welagen J, van der Drift C, Jetten MSM, Burton K, Van Griensven LJLD, Op den Camp HJM. The role of ornithine aminotransferase in fruiting body formation of the mushroom Agaricus bisporus. ACTA ACUST UNITED AC 2007; 111:909-18. [PMID: 17703933 DOI: 10.1016/j.mycres.2007.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
The complete oat gene and cDNA from the commercial mushroom, Agaricus bisporus, encoding ornithine aminotransferase (OAT) was characterized. The gene encodes a 466 amino acid protein and provides the first fully reported homobasidiomycete OAT protein sequence. The gene is interrupted by ten introns, and no mitochondrial targeting motif was present pointing to a cytoplasmic localization. The function of the gene was demonstrated by complementation of a Saccharomyces cerevisiae mutant unable to utilize ornithine as a sole source of nitrogen with an A. bisporus oat cDNA construct. Northern analysis of the oat gene together with the pruA gene (encoding Delta(1)-pyrroline-5-carboxylate dehydrogenase) showed that transcripts of both genes were lower during the first stages of fruiting body development. The higher expression of the oat gene in later stages of development, suggests the importance of ornithine metabolism for the redistribution of metabolites in the developing mushroom. Hplc analysis of all amino acids revealed that ornithine levels increased during fruiting body development whereas proline levels fell.
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Affiliation(s)
- Matthijs J M Wagemaker
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
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30
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Dufe V, Ingner D, Heby O, Khomutov A, Persson L, Al-Karadaghi S. A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane. Biochem J 2007; 405:261-8. [PMID: 17407445 PMCID: PMC1904517 DOI: 10.1042/bj20070188] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The critical role of polyamines in key processes such as cell growth, differentiation and macromolecular synthesis makes the enzymes involved in their synthesis potential targets in the treatment of certain types of cancer and parasitic diseases. Here we present a study on the inhibition of human and Leishmania donovani ODC (ornithine decarboxylase), the first committed enzyme in the polyamine biosynthesis pathway, by APA (1-amino-oxy-3-aminopropane). The present study shows APA to be a potent inhibitor of both human and L. donovani ODC with a K(i) value of around 1.0 nM. We also show that L. donovani ODC binds the substrate, the co-enzyme pyridoxal 5'-phosphate and the irreversible inhibitor alpha-difluoromethylornithine (a curative agent of West African sleeping sickness) with less affinity than human ODC. We have also determined the three-dimensional structure of human ODC in complex with APA, which revealed the mode of the inhibitor binding to the enzyme. In contrast with earlier reports, the structure showed no indication of oxime formation between APA and PLP (pyridoxal 5'-phosphate). Homology modelling suggests a similar mode of binding of APA to L. donovani ODC. A comparison of the ODC-APA-PLP structure with earlier ODC structures also shows that the protease-sensitive loop (residues 158-168) undergoes a large conformational change and covers the active site of the protein. The understanding of the structural mode of APA binding may constitute the basis for the development of more specific inhibitors of L. donovani ODC.
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Affiliation(s)
- Veronica T. Dufe
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
| | - Daniel Ingner
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
| | - Olle Heby
- †Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden
| | - Alex R. Khomutov
- ‡Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lo Persson
- §Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden
- Correspondence may be addressed to either of these authors (email or )
| | - Salam Al-Karadaghi
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
- Correspondence may be addressed to either of these authors (email or )
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Sekhar PN, Amrutha RN, Sangam S, Verma DPS, Kishor PBK. Biochemical characterization, homology modeling and docking studies of ornithine delta-aminotransferase--an important enzyme in proline biosynthesis of plants. J Mol Graph Model 2007; 26:709-19. [PMID: 17604199 DOI: 10.1016/j.jmgm.2007.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Revised: 04/27/2007] [Accepted: 04/28/2007] [Indexed: 11/28/2022]
Abstract
Ornithine delta-aminotransferase (OAT) is an important enzyme in proline biosynthetic pathway and is implicated in salt tolerance in higher plants. OAT transaminates ornithine to pyrroline 5-carboxylate, which is further catalyzed to proline by pyrroline 5-carboxylate reductase. The Vigna aconitifolia OAT cDNA, encoding a polypeptide of 48.1 kDa, was expressed in Escherichia coli and the enzyme was partially characterized following its purification using (NH(4))(2)SO(4) precipitation and gel filtration techniques. Optimal activity of the enzyme was observed at a temperature of 25 degrees C and pH 8.0. The enzyme appeared to be a monomer and exhibited high activity at 4mM ornithine. Proline did not show any apparent effect but isoleucine, valine and serine inhibited the activity when added into the assay mixture along with ornithine. Omission of pyridoxal 5'-phosphate from the reaction mixture reduced the activity of this enzyme by 60%. To further evaluate these biochemical observations, homology modeling of the OAT was performed based on the crystal structure of the ornithine delta-aminotransferase from humans (PDB code 1OAT) by using the software MODELLER6v2. With the aid of the molecular mechanics and dynamics methods, the final model was obtained and assessed subsequently by PROCHECK and VERIFY-3D graph. With this model, a flexible docking study with the substrate and inhibitors was performed and the results indicated that Gly106 and Lys256 in OAT are the important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate and inhibitors. These observations are in conformity with the results obtained from experimental investigations.
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Affiliation(s)
- P Nataraj Sekhar
- Department of Genetics, Osmania University, Hyderabad 500007, India
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Abstract
Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.
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Affiliation(s)
- Carmen Drahl
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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Rajaram V, Prasad K, Ratna Prasuna P, Ramachandra N, Bharath SR, Savithri HS, Murthy MRN. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the biosynthetic N-acetylornithine aminotransferases from Salmonella typhimurium and Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:980-3. [PMID: 17012789 PMCID: PMC2225180 DOI: 10.1107/s1744309106033884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/23/2006] [Indexed: 11/11/2022]
Abstract
Acetylornithine aminotransferase (AcOAT) is a type I pyridoxal 5'-phosphate-dependent enzyme catalyzing the conversion of N-acetylglutamic semialdehyde to N-acetylornithine in the presence of alpha-ketoglutarate, a step involved in arginine metabolism. In Escherichia coli, the biosynthetic AcOAT also catalyzes the conversion of N-succinyl-L-2-amino-6-oxopimelate to N-succinyl-L,L-diaminopimelate, one of the steps in lysine biosynthesis. It is closely related to ornithine aminotransferase. AcOAT was cloned from Salmonella typhimurium and E. coli, overexpressed in E. coli and purified using Ni-NTA affinity column chromatography. The enzymes crystallized in the presence of gabaculine. Crystals of E. coli AcOAT (eAcOAT) only diffracted X-rays to 3.5 A and were twinned. The crystals of S. typhimurium AcOAT (sAcOAT) diffracted to 1.9 A and had a dimer in the asymmetric unit. The structure of sAcOAT was solved by the molecular-replacement method.
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Affiliation(s)
- V. Rajaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - K. Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - P. Ratna Prasuna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - N. Ramachandra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - S. R. Bharath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - H. S. Savithri
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - M. R. N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- Correspondence e-mail:
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Tocilj A, Schrag JD, Li Y, Schneider BL, Reitzer L, Matte A, Cygler M. Crystal Structure of N-Succinylarginine Dihydrolase AstB, Bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli. J Biol Chem 2005; 280:15800-8. [PMID: 15703173 DOI: 10.1074/jbc.m413833200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ammonia-producing arginine succinyltransferase pathway is the major pathway in Escherichia coli and related bacteria for arginine catabolism as a sole nitrogen source. This pathway consists of five steps, each catalyzed by a distinct enzyme. Here we report the crystal structure of N-succinylarginine dihydrolase AstB, the second enzyme of the arginine succinyltransferase pathway, providing the first structural insight into enzymes from this pathway. The enzyme exhibits a pseudo 5-fold symmetric alpha/beta propeller fold of circularly arranged betabetaalphabeta modules enclosing the active site. The crystal structure indicates clearly that this enzyme belongs to the amidinotransferase (AT) superfamily and that the active site contains a Cys-His-Glu triad characteristic of the AT superfamily. Structures of the complexes of AstB with the reaction product and a C365S mutant with bound the N-succinylarginine substrate suggest a catalytic mechanism that consists of two cycles of hydrolysis and ammonia release, with each cycle utilizing a mechanism similar to that proposed for arginine deiminases. Like other members of the AT superfamily of enzymes, AstB possesses a flexible loop that is disordered in the absence of substrate and assumes an ordered conformation upon substrate binding, shielding the ligand from the bulk solvent, thereby controlling substrate access and product release.
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Affiliation(s)
- Ante Tocilj
- Biotechnology Research Institute, Montréal, Québec H4P 2R2, Canada
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36
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Abstract
Pyridoxal phosphate (PLP)-dependent enzymes are unrivaled in the diversity of reactions that they catalyze. New structural data have paved the way for targeted mutagenesis and mechanistic studies and have provided a framework for interpretation of those results. Together, these complementary approaches yield new insight into function, particularly in understanding the origins of substrate and reaction type specificity. The combination of new sequences and structures enables better reconstruction of their evolutionary heritage and illuminates unrecognized similarities within this diverse group of enzymes. The important metabolic roles of many PLP-dependent enzymes drive efforts to design specific inhibitors, which are now guided by the availability of comprehensive structural and functional databases. Better understanding of the function of this important group of enzymes is crucial not only for inhibitor design, but also for the design of improved protein-based catalysts.
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Affiliation(s)
- Andrew C Eliot
- Department of Chemistry University of California, Berkeley, California 94720-3206, USA.
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Terwilliger TC. Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2003; 59:1174-82. [PMID: 12832760 PMCID: PMC2745880 DOI: 10.1107/s0907444903009922] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2003] [Accepted: 05/06/2003] [Indexed: 11/15/2022]
Abstract
An iterative process for improving the completeness and quality of atomic models automatically built at moderate resolution (up to about 2.8 A) is described. The process consists of cycles of model building interspersed with cycles of refinement and combining phase information from the model with experimental phase information (if any) using statistical density modification. The process can lead to substantial improvements in both the accuracy and completeness of the model compared with a single cycle of model building. For eight test cases solved by MAD or SAD at resolutions ranging from 2.0 to 2.8 A, the fraction of models built and assigned to sequence was 46-91% (mean of 65%) after the first cycle of building and refinement, and 78-95% (mean of 87%) after 20 cycles. In an additional test case, an incorrect model of gene 5 protein (PDB code 2gn5; r.m.s.d. of main-chain atoms from the more recent refined structure 1vqb at 1.56 A) was rebuilt using only structure-factor amplitude information at varying resolutions from 2.0 to 3.0 A. Rebuilding was effective at resolutions up to about 2.5 A. The resulting models had 60-80% of the residues built and an r.m.s.d. of main-chain atoms from the refined structure of 0.20 to 0.62 A. The algorithm is useful for building preliminary models of macromolecules suitable for an experienced crystallographer to extend, correct and fully refine.
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Mann S, Lesage D, Tabet JC, Marquet A. Identification of the products of reaction between pyridoxal phosphate and amiclenomycin and other related 1-amino-cyclohexa-2,5-dienes. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00782-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Sandmark J, Mann S, Marquet A, Schneider G. Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin. J Biol Chem 2002; 277:43352-8. [PMID: 12218056 DOI: 10.1074/jbc.m207239200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antibiotic amiclenomycin blocks the biosynthesis of biotin by inhibiting the pyridoxal-phosphate-dependent enzyme diaminopelargonic acid synthase. Inactivation of the enzyme is stereoselective, i.e. the cis isomer of amiclenomycin is a potent inhibitor, whereas the trans isomer is much less reactive. The crystal structure of the complex of the holoenzyme and amiclenomycin at 1.8 A resolution reveals that the internal aldimine linkage between the cofactor and the side chain of the catalytic residue Lys-274 is broken. Instead, a covalent bond is formed between the 4-amino nitrogen of amiclenomycin and the C4' carbon atom of pyridoxal-phosphate. The electron density for the bound inhibitor suggests that aromatization of the cyclohexadiene ring has occurred upon formation of the covalent adduct. This process could be initiated by proton abstraction at the C4 carbon atom of the cyclohexadiene ring, possibly by the proximal side chain of Lys-274, leading to the tautomer Schiff base followed by the removal of the second allylic hydrogen. The carboxyl tail of the amiclenomycin moiety forms a salt link to the conserved residue Arg-391 in the substrate-binding site. Modeling suggests steric hindrance at the active site as the determinant of the weak inhibiting potency of the trans isomer.
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Affiliation(s)
- Jenny Sandmark
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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40
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Noland BW, Newman JM, Hendle J, Badger J, Christopher JA, Tresser J, Buchanan MD, Wright TA, Rutter ME, Sanderson WE, Müller-Dieckmann HJ, Gajiwala KS, Buchanan SG. Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. Structure 2002; 10:1569-80. [PMID: 12429098 DOI: 10.1016/s0969-2126(02)00879-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
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41
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Gafan C, Wilson J, Berger LC, Berger BJ. Characterization of the ornithine aminotransferase from Plasmodium falciparum. Mol Biochem Parasitol 2001; 118:1-10. [PMID: 11704268 DOI: 10.1016/s0166-6851(01)00357-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The ornithine aminotransferase from Plasmodium falciparum 3D7 was cloned, functionally expressed, and characterized. The gene exists as a single copy in the malarial genome and is located on chromosomes 6/7/8. The deduced amino acid sequence was found to be 85% identical to a similar sequence discovered in Plasmodium yoelii, 82% identical to a partial sequence from Plasmodium vivax, and 42-53% identical to ornithine aminotransferases from other eukaryotes. The enzyme had a very narrow substrate specificity, and could only catalyze the transamination of alpha-ketoglutarate with ornithine or N-acetylornithine, and of glutamate-5-semialdehyde with glutamate and alanine. The aminooxy analogue of ornithine, canaline, was found to inhibit the ornithine aminotransferase uncompetatively with a Ki of 492+/-98 nM. As the enzyme effectively catalyzed both ornithine catabolism and formation, its potential role in ornithine biosynthesis from glutamine, via glutamate, glutamate-5-phosphate, and glutamate-5-semialdehyde, was examined. Over the course of a 3.5 h incubation, P. falciparum converted 34% of exogenous, radiolabeled glutamine to glutamate and 0.68% to ornithine. This low level of conversion suggests that the parasite may have alternative mechanisms for obtaining ornithine for polyamine biosynthesis.
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Affiliation(s)
- C Gafan
- Department of Biochemistry, University of Dundee, DD1 5EH, Dundee, UK
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42
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Metzler DE, Metzler CM, Sauke DJ. The Metabolism of Nitrogen and Amino Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Metzler DE, Metzler CM, Sauke DJ. Coenzymes. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Abstract
Pyridoxal-5'-phosphate (vitamin B6) binding enzymes form a large superfamily that contains at least five different folds. The availability of an increasing number of known three-dimensional structures for members of this superfamily has allowed a detailed structural classification. Most progress has been made with the fold type I or aspartate aminotransferase family.
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Affiliation(s)
- G Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, S-171 77, Sweden.
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45
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Capitani G, Hohenester E, Feng L, Storici P, Kirsch JF, Jansonius JN. Structure of 1-aminocyclopropane-1-carboxylate synthase, a key enzyme in the biosynthesis of the plant hormone ethylene. J Mol Biol 1999; 294:745-56. [PMID: 10610793 DOI: 10.1006/jmbi.1999.3255] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 2.4 A crystal structure of the vitamin B6-dependent enzyme 1-aminocyclopropane-1-carboxylate (ACC) synthase is described. This enzyme catalyses the committed step in the biosynthesis of ethylene, a plant hormone that is responsible for the initiation of fruit ripening and for regulating many other developmental processes. ACC synthase has 15 % sequence identity with the well-studied aspartate aminotransferase, and a completely different catalytic activity yet the overall folds and the active sites are very similar. The new structure together with available biochemical data enables a comparative mechanistic analysis that largely explains the catalytic roles of the conserved and non-conserved active site residues. An external aldimine reaction intermediate (external aldimine with ACC, i.e. with the product) has been modeled. The new structure provides a basis for the rational design of inhibitors with broad agricultural applications.
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Affiliation(s)
- G Capitani
- Structural Biology Division Biozentrum, University of Basel, Basel, CH-4056, Switzerland.
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46
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Malashkevich VN, Strop P, Keller JW, Jansonius JN, Toney MD. Crystal structures of dialkylglycine decarboxylase inhibitor complexes. J Mol Biol 1999; 294:193-200. [PMID: 10556038 DOI: 10.1006/jmbi.1999.3254] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.
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Affiliation(s)
- V N Malashkevich
- Department of Structural Biology, Biozentrum University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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47
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Poupon A, Jebai F, Labesse G, Gros F, Thibault J, Mornon JP, Krieger M. Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study. Proteins 1999; 37:191-203. [PMID: 10584065 DOI: 10.1002/(sici)1097-0134(19991101)37:2<191::aid-prot5>3.0.co;2-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pyridoxal-5'-phosphate-dependent enzymes (B6 enzymes) are grouped into three main families named alpha, beta, and gamma. Proteins in the alpha and gamma families share the same fold and might be distantly related, while those in the beta family exhibit specific structural features. The rat aromatic L-amino acid decarboxylase (AADC; EC(4.1.1.28)) catalyzes the synthesis of two important neurotransmitters: dopamine and serotonin. It binds the cofactor pyridoxal-5'-phosphate and belongs to the alpha family. Despite the low level of sequence identity (approximately 10%) shared by the rat AADC and the sequences of the enzymes belonging to the B6 enzymes family, including the known three-dimensional structures, a multiple sequence alignment was deduced. A model was built using segments belonging to seven of the eleven known structures. By homology, and based on knowledge of the biochemistry of the aspartate aminotransferase, structurally and functionally important residues were identified in the rat AADC. Site-directed mutagenesis of the conserved residues D271, T246, and C311 was carried out in order to confirm our predictions and highlight their functional role. Mutation of D271A and D271N resulted in complete loss of enzyme activity, while the D271E mutant exhibited 2% of the wild-type activity. Substitution of T246A resulted in 5% of the wild-type activity while the C311A mutant conserved 42% of the wild-type activity. A functional model of the AADC is discussed in view of the structural model and the complementary mutagenesis and labelling studies.
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Affiliation(s)
- A Poupon
- Laboratoire de Minéralogie-Cristallographie, CNRS, Université, Paris VI, France.
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48
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Käck H, Sandmark J, Gibson K, Schneider G, Lindqvist Y. Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes. J Mol Biol 1999; 291:857-76. [PMID: 10452893 DOI: 10.1006/jmbi.1999.2997] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The structure was solved by multi-wavelength anomalous diffraction techniques using a crystal derivatized with mercury ions. The protein model has been refined to a crystallographic R -value of 17.5% (R -free 22.6%). Each enzyme subunit consists of two domains, a large domain (residues 50-329) containing a seven-stranded predominantly parallel beta-sheet, surrounded by alpha-helices, and a small domain comprising residues 1-49 and 330-429. Two subunits, related by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domain of the second subunit. The cofactor is anchored to the enzyme by a covalent linkage to the side-chain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113, located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na(+), was found in a tight turn at the surface of the enzyme. Structure analysis reveals that diaminopelargonic acid synthase belongs to the family of vitamin B6-dependent aminotransferases with the same fold as originally observed in aspartate aminotransferase. A multiple structure alignment of enzymes in this family indicated that they form at least six different subclasses. Striking differences in the fold of the N-terminal part of the polypeptide chain are one of the hallmarks of these subclasses. Diaminopelargonic acid synthase is a member of the aminotransferase subclass III. From the structure of the non-productive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate binding have been identified.
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Affiliation(s)
- H Käck
- Division of Structural Biology Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Doktorsringen 9, Stockholm, S-171 77, Sweden
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49
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Fu M, Silverman RB. Isolation and characterization of the product of inactivation of gamma-aminobutyric acid aminotransferase by gabaculine. Bioorg Med Chem 1999; 7:1581-90. [PMID: 10482450 DOI: 10.1016/s0968-0896(99)00081-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gabaculine (5-amino-1,3-cyclohexadienylcarboxylic acid, 1), a naturally occurring neurotoxin isolated from Streptomyces toyocaenis, has been shown to be a mechanism-based inactivator of gamma-aminobutyric acid aminotransferase (GABA-AT) (Rando, R. R. Biochemistry 1977, 16, 4604). Inactivation results from reaction of gabaculine with the pyridoxal 5'-phosphate (PLP) cofactor. Two HPLC systems for isolating this inactivator-PLP adduct are described as well as a detailed characterization of the adduct, including the ultraviolet-visible spectrum, electrospray mass spectra, and NMR spectrum. The same spectral characterization of the chemically synthesized gabaculine-PLP adduct is also reported.
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Affiliation(s)
- M Fu
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA
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50
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Shah SA, Brunger AT. The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure. J Mol Biol 1999; 285:1577-88. [PMID: 9917398 DOI: 10.1006/jmbi.1998.2385] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of a 17 base RNA oligomer, r(CACCGGAUG GUUCGGUG), has been solved to a resolution of 1.8 A through a combination of molecular replacement, multiple isomorphous replacement phasing, and analysis of observed intensity distributions. The oligomer, which forms a stem-loop in solution, crystallized as a pseudo-infinite duplex in spacegroup P321. The asymmetric unit of the crystal contains four superimposed orientations of the duplex that are out of register, such that backbones superimpose, but base identity differs. This static disorder was initially discovered by brominating a single residue per strand in the sequence, and observing four peaks per strand in difference maps phased with a native molecular replacement solution. The presence of four superimposed duplex "motifs" related by non-crystallographic hypersymmetry was detected by computing <I2>/<I>2 and Wilson ratios for the observed intensities. The observed ratios matched those produced from calculated intensities of a 4-fold statically disordered model. Multi-conformer simulated annealing refinement against a maximum-likelihood target incorporating experimental phase information was used to refine the 4-fold disordered model to an Rfree and R of 29.35% and 25.5%, respectively. The resulting structure reveals four distinct conformations of the duplex, with an average pairwise backbone rmsd of 2.35 A. The structural differences between the four conformations, which can be attributed to differences in packing environment, highlight the possible influence of crystal packing forces on nucleic acid X-ray structures. Analysis of inter-helical packing between symmetry-related molecules reveals an RNA "zipper" that mediates direct phosphate oxygen-2' hydroxyl interactions between close-packed phosphate-sugar backbones. This may be a general mode for RNA tertiary interaction that does not depend on metal ions or primary sequence.
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Affiliation(s)
- S A Shah
- Department of Molecular Biophysics and Biochemistry
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