1
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Wandrey N, Hamilton L, Boley J, Haynes A, Redinger M, Hill M, Hagemeister M, Cole PA, Moxley MA, Thomas AA. AANAT kinetics of CoASH-targeted electrophiles of tryptamine and related analogs. Bioorg Med Chem Lett 2024; 113:129975. [PMID: 39332648 DOI: 10.1016/j.bmcl.2024.129975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/09/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
Arylalkylamine N-acetyltransferase (AANAT) catalyzes the rate-limiting step in melatonin synthesis and is a potential target for disorders involving melatonin overproduction, such as seasonal affective disorder. Previously described AANAT inhibitor bromoacetyltryptamine (BAT) and benzothiophenes analogs were reported to react with CoASH to form potent bisubstrate inhibitors through AANAT's alkyltransferase function, which is secondary to its role as an acetyltransferase. We replaced the bromoacetyl group in BAT with various Michael acceptors to mitigate possible off-target activity of its bromoacetyl group. Additionally, we modified the length of the carbon linker between the Michael acceptor and indole bicycle of tryptamine to determine its effect on potency. An AANAT enzymatic assay showed a two-carbon linker present in BAT was optimal, while none of the new warheads had activity. Kinetic analysis indicated that these Michael acceptors reacted with CoASH much slower than BAT and not within the timeframe of our enzymatic assay. Additionally, we confirmed earlier reports that the acetyltransferase function of AANAT follows an ordered bi bi mechanism in which AcCoA binds before serotonin. In contrast, BAT's alkyltransferase kinetics revealed a bi uni mechanism in which BAT binds to AANAT before CoASH. Our model combines both functions of AANAT into one kinetic mechanism.
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Affiliation(s)
- Nicole Wandrey
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Luke Hamilton
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Jake Boley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Alexis Haynes
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Makenna Redinger
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Mackinzi Hill
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Moxley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA
| | - Allen A Thomas
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE 69949, USA.
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2
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Jiang H, Miller BD, Viennet T, Kim H, Lee K, Arthanari H, Cole PA. Protein semisynthesis reveals plasticity in HECT E3 ubiquitin ligase mechanisms. Nat Chem 2024:10.1038/s41557-024-01576-z. [PMID: 39030419 DOI: 10.1038/s41557-024-01576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/11/2024] [Indexed: 07/21/2024]
Abstract
Lys ubiquitination is catalysed by E3 ubiquitin ligases and is central to the regulation of protein stability and cell signalling in normal and disease states. There are gaps in our understanding of E3 mechanisms, and here we use protein semisynthesis, chemical rescue, microscale thermophoresis and other biochemical approaches to dissect the role of catalytic base/acid function and conformational interconversion in HECT-domain E3 catalysis. We demonstrate that there is plasticity in the use of the terminal side chain or backbone carboxylate for proton transfer in HECT E3 ubiquitin ligase reactions, with yeast Rsp5 orthologues appearing to be possible evolutionary intermediates. We also show that the HECT-domain ubiquitin covalent intermediate appears to eject the E2 conjugating enzyme, promoting catalytic turnover. These findings provide key mechanistic insights into how protein ubiquitination occurs and provide a framework for understanding E3 functions and regulation.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bryant D Miller
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Human Biology, Sattler College, Boston, MA, USA
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Hyojeon Kim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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3
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Wang Q, Li C, Yuan B, Yu A, Qu G, Sun Z. Engineering the Activity of a Newly Identified Arylalkylamine N-Acetyltransferase in the Acetylation of 5-Hydroxytryptamine. Chembiochem 2024; 25:e202400069. [PMID: 38504591 DOI: 10.1002/cbic.202400069] [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: 01/25/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Arylalkylamine N-acetyltransferase (AANAT) serves as a key enzyme in the biosynthesis of melatonin by transforming 5-hydroxytryptamine (5-HT) to N-acetyl-5-hydroxytryptamine (NAS), while its low activity may hinder melatonin yield. In this study, a novel AANAT derived from Sus scrofa (SsAANAT) was identified through data mining using 5-HT as a model substrate, and a rational design of SsAANAT was conducted in the quest to improving its activity. After four rounds of mutagenesis procedures, a triple combinatorial dominant mutant M3 was successfully obtained. Compared to the parent enzyme, the conversion of the whole-cell reaction bearing the best variant M3 exhibted an increase from 50 % to 99 % in the transformation of 5-HT into NAS. Additionally, its catalytic efficiency (kcat/Km) was enhanced by 2-fold while retaining the thermostability (Tm>45 °C). In the up-scaled reaction with a substrate loading of 50 mM, the whole-cell system incorporating variant M3 achieved a 99 % conversion of 5-HT in 30 h with an 80 % yield. Molecular dynamics simulations were ultilized to shed light on the origin of improved activity. This study broadens the repertoire of AANAT for the efficient biosynthesis of melatonin.
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Affiliation(s)
- Qing Wang
- College of Biotechnology, Tianjin University of Science and Technology, 300457, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, 300308, Tianjin, China
| | - Congcong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, 300308, Tianjin, China
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Aiqun Yu
- College of Biotechnology, Tianjin University of Science and Technology, 300457, Tianjin, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
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4
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Hagemeister M, Hamilton L, Wandrey N, Hill M, Mounce E, Mosel N, Lytle K, Redinger M, Boley J, Fancher N, Haynes A, Fill I, Cole PA, Hill E, Moxley MA, Thomas AA. Evaluation of Rhodanine Indolinones as AANAT Inhibitors. ChemMedChem 2024; 19:e202300567. [PMID: 37984928 PMCID: PMC10843758 DOI: 10.1002/cmdc.202300567] [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: 10/19/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/22/2023]
Abstract
Circadian rhythm (CR) dysregulation negatively impacts health and contributes to mental disorders. The role of melatonin, a hormone intricately linked to CR, is still a subject of active study. The enzyme arylalkylamine N-acetyltransferase (AANAT) is responsible for melatonin synthesis, and it is a potential target for disorders that involve abnormally high melatonin levels, such as seasonal affective disorder (SAD). Current AANAT inhibitors suffer from poor cell permeability, selectivity, and/or potency. To address the latter, we have employed an X-ray crystal-based model to guide the modification of a previously described AANAT inhibitor, containing a rhodanine-indolinone core. We made various structural modifications to the core structure, including testing the importance of a carboxylic acid group thought to bind in the CoA site, and we evaluated these changes using MD simulations in conjunction with enzymatic assay data. Additionally, we tested three AANAT inhibitors in a zebrafish locomotion model to determine their effects in vivo. Key discoveries were that potency could be modestly improved by replacing a 5-carbon alkyl chain with rings and that the central rhodanine ring could be replaced by other heterocycles and maintain potency.
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Affiliation(s)
- Mackenzie Hagemeister
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Luke Hamilton
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Nicole Wandrey
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Mackinzi Hill
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Emery Mounce
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Noah Mosel
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Katie Lytle
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Makenna Redinger
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Jake Boley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Nathan Fancher
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Alexis Haynes
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Ianna Fill
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Philip A Cole
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Hill
- Department of Psychology, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Michael A Moxley
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
| | - Allen A Thomas
- Department of Chemistry, University of Nebraska at Kearney, Kearney, NE, 69949, USA
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5
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Méjean A, Lequin O, Ploux O. Identification of 7-Deoxy-desulfo-argino-cylindrospermopsin, the Missing Piece in Cylindrospermopsin Biosynthesis. J Am Chem Soc 2022; 144:14627-14637. [PMID: 35916199 DOI: 10.1021/jacs.2c03932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cylindrospermopsin, a major cyanotoxin, is produced by freshwater cyanobacteria. Its biosynthesis starts from arginine and glycine and involves five polyketide synthases and several tailoring enzymes. We report the identification of 7-deoxy-desulfo-argino-cylindrospermopsin in several cylindrospermopsin-producing cyanobacteria using mass spectrometry experiments. We have purified this new metabolite and established its structure by 1D and 2D NMR spectroscopy using scalar-based 1H-1H, 1H-13C, and 1H-15N as well as 2D 1H-1H ROESY correlation experiments. Using labeled arginines in isotopic incorporation experiments, we have shown that arginine is fully incorporated into 7-deoxy-desulfo-argino-cylindrospermopsin and that the uracil ring of cylindrospermopsin originates from the guanidino moiety of arginine, thus solving a long-standing puzzling question. CyrG and CyrH from the cylindrospermopsin-producing Oscillatoria sp. PCC 6506 were overproduced in Escherichia coli and purified to homogeneity. We showed that CyrG is a zinc-dependent hydrolase, homologous to adenosine deaminases, that transforms 7-deoxy-desulfo-argino-cylindrospermopsin into 7-deoxy-desulfo-cylindrospermopsin and ornithine, with the following kinetic parameters: KM = 0.21 ± 0.05 μM and kcat = 0.19 ± 0.02 min-1. CyrG contained 0.55 mol of zinc per mol of monomer but could be activated by FeII or CoII. CyrH contained almost no metal and showed no such activity even in the presence of excess metal. Using structure-based alignments and secondary structure predictions, we propose that the fifth and last polyketide synthase CyrF in cylindrospermopsin biosynthesis contains an unprecedented C-terminal domain homologous to N-acetyltransferases. We suggest that this domain catalyzes the condensation of the CyrF product with arginine to give 7-deoxy-desulfo-argino-cylindrospermopsin. This would be an unprecedented termination step for a polyketide synthase.
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Affiliation(s)
- Annick Méjean
- LIED, UMR 8236 CNRS, Université Paris Cité, 75205 Paris Cedex 13, France
| | - Olivier Lequin
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Olivier Ploux
- LIED, UMR 8236 CNRS, Université Paris Cité, 75205 Paris Cedex 13, France.,Chimie ParisTech, PSL, 75005 Paris, France
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6
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Huang Y, Li J, Bian C, Li R, You X, Shi Q. Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish. Front Genet 2022; 13:820442. [PMID: 35664299 PMCID: PMC9160868 DOI: 10.3389/fgene.2022.820442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
As an important hormone, melatonin participates in endocrine regulation of diverse functions in vertebrates. Its biosynthesis is catalyzed by four cascaded enzymes, among them, arylalkylamine N-acetyltransferase (AANAT) is the most critical one. Although only single aanat gene has been identified in most groups of vertebrates, researchers including us have determined that fish have the most diverse of aanat genes (aanat1a, aanat1b, and aanat2), playing various potential roles such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. With the rapid development of genome and transcriptome sequencing, more and more putative sequences of fish aanat genes are going to be available. Related phylogeny and functional investigations will enrich our understanding of AANAT functions in various fish species.
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Affiliation(s)
- Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-Ugent Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
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7
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Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. J Chem Inf Model 2021; 61:1287-1299. [PMID: 33599485 DOI: 10.1021/acs.jcim.0c01002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein dynamics play an important role in small molecule binding and can pose a significant challenge in the identification of potential binding sites. Cryptic binding sites have been defined as sites which require significant rearrangement of the protein structure to become physically accessible to a ligand. Mixed-solvent MD (MixMD) is a computational protocol which maps the surface of the protein using molecular dynamics (MD) of the unbound protein solvated in a 5% box of probe molecules with explicit water. This method has successfully identified known active and allosteric sites which did not require reorganization. In this study, we apply the MixMD protocol to identify known cryptic sites of 12 proteins characterized by a wide range of conformational changes. Of these 12 proteins, three require reorganization of side chains, five require loop movements, and four require movement of more significant structures such as whole helices. In five cases, we find that standard MixMD simulations are able to map the cryptic binding sites with at least one probe type. In two cases (guanylate kinase and TIE-2), accelerated MD, which increases sampling of torsional angles, was necessary to achieve mapping of portions of the cryptic binding site missed by standard MixMD. For more complex systems where movement of a helix or domain is necessary, MixMD was unable to map the binding site even with accelerated dynamics, possibly due to the limited timescale (100 ns for individual simulations). In general, similar conformational dynamics are observed in water-only simulations and those with probe molecules. This could imply that the probes are not driving opening events but rather take advantage of mapping sites that spontaneously open as part of their inherent conformational behavior. Finally, we show that docking to an ensemble of conformations from the standard MixMD simulations performs better than docking the apo crystal structure in nine cases and even better than half of the bound crystal structures. Poorer performance was seen in docking to ensembles of conformations from the accelerated MixMD simulations.
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Affiliation(s)
- Richard D Smith
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1056, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1056, United States
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8
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Choi WS, Liu B, Shen Z, Yang W. Structure of human BCCIP and implications for binding and modification of partner proteins. Protein Sci 2021; 30:693-699. [PMID: 33452718 DOI: 10.1002/pro.4026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 11/09/2022]
Abstract
BCCIP was isolated based on its interactions with tumor suppressors BRCA2 and p21. Knockdown or knockout of BCCIP causes embryonic lethality in mice. BCCIP deficient cells exhibit impaired cell proliferation and chromosome instability. BCCIP also plays a key role in biogenesis of ribosome 60S subunits. BCCIP is conserved from yeast to humans, but it has no discernible sequence similarity to proteins of known structures. Here we report two crystal structures of an N-terminal truncated human BCCIPβ, consisting of residues 61-314. Structurally BCCIP is similar to GCN5-related acetyltransferases (GNATs) but contains different sequence motifs. Moreover, both acetyl-CoA and substrate-binding grooves are altered in BCCIP. A large 19-residue flap over the putative CoA binding site adopts either an open or closed conformation in BCCIP. The substrate binding groove is significantly reduced in size and is positively charged despite the acidic isoelectric point of BCCIP. BCCIP has potential binding sites for partner proteins and may have enzymatic activity.
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Affiliation(s)
- Woo Suk Choi
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
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9
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O'Flynn BG, Prins KC, Shepherd BA, Forbrich VE, Suarez G, Merkler DJ. Identification of catalytically distinct arylalkylamine N-acetyltransferase splicoforms from Tribolium castaneum. Protein Expr Purif 2020; 175:105695. [PMID: 32681959 DOI: 10.1016/j.pep.2020.105695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/18/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
The assumption that structural or sequential homology between enzymes implies functional homology is a common misconception. Through in-depth structural and kinetic analysis, we are now beginning to understand the minute differences in primary structure that can alter the function of an enzyme completely. Alternative splicing is one method for which the activity of an enzyme can be controlled, simply by altering its length. Arylalkylamine N-acetyltransferase A (AANATA) in D. melanogaster, which catalyzes the N-acetylation of biogenic amines, has multiple splicoforms - alternatively spliced enzyme isoforms - with differing tissue distribution. As demonstrated here, AANAT1 from Tribolium castaneum is another such enzyme with multiple splicoforms. A screening assay was developed and utilized to determine that, despite only a 35 amino acid truncation, the shortened form of TcAANAT1 is a more active form of the enzyme. This implies regulation of enzyme metabolic activity via alternative splicing.
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Affiliation(s)
- Brian G O'Flynn
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Karin Claire Prins
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Britney A Shepherd
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | | | - Gabriela Suarez
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - David J Merkler
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA.
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10
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Reidl C, Majorek KA, Dang J, Tran D, Jew K, Law M, Payne Y, Minor W, Becker DP, Kuhn ML. Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases. FEBS Lett 2017; 591:2348-2361. [PMID: 28703494 PMCID: PMC5578807 DOI: 10.1002/1873-3468.12753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 01/07/2023]
Abstract
Gcn5-related N-acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor-bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X-ray induced radical-mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely applicable across the GNAT superfamily and can be used to improve the success rate of obtaining liganded structures of other acyltransferases.
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Affiliation(s)
- Cory Reidl
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Karolina A Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Joseph Dang
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - David Tran
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Kristen Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | - Yasmine Payne
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Daniel P. Becker
- Loyola University Chicago, Department of Chemistry, 1032 W. Sheridan Rd., Chicago, IL 60660, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
| | - Misty L. Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA,To whom correspondence may be addressed: Either Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132. Tel.: 415-405-2112; or Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, IL 60660, Tel.: 773-508-3089;
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11
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Salah Ud-Din AIM, Tikhomirova A, Roujeinikova A. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Int J Mol Sci 2016; 17:E1018. [PMID: 27367672 PMCID: PMC4964394 DOI: 10.3390/ijms17071018] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Alexandra Tikhomirova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
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12
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Dempsey DR, Jeffries KA, Handa S, Carpenter AM, Rodriguez-Ospina S, Breydo L, Merkler DJ. Mechanistic and Structural Analysis of a Drosophila melanogaster Enzyme, Arylalkylamine N-Acetyltransferase Like 7, an Enzyme That Catalyzes the Formation of N-Acetylarylalkylamides and N-Acetylhistamine. Biochemistry 2015; 54:2644-58. [PMID: 25850002 DOI: 10.1021/acs.biochem.5b00113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Arylalkylamine N-acetyltransferase like 7 (AANATL7) catalyzes the formation of N-acetylarylalkylamides and N-acetylhistamine from acetyl-CoA and the corresponding amine substrate. AANATL7 is a member of the GNAT superfamily of >10000 GCN5-related N-acetyltransferases, many members being linked to important roles in both human metabolism and disease. Drosophila melanogaster utilizes the N-acetylation of biogenic amines for the inactivation of neurotransmitters, the biosynthesis of melatonin, and the sclerotization of the cuticle. We have expressed and purified D. melanogaster AANATL7 in Escherichia coli and used the purified enzyme to define the substrate specificity for acyl-CoA and amine substrates. Information about the substrate specificity provides insight into the potential contribution made by AANATL7 to fatty acid amide biosynthesis because D. melanogaster has emerged as an important model system contributing to our understanding of fatty acid amide metabolism. Characterization of the kinetic mechanism of AANATL7 identified an ordered sequential mechanism, with acetyl-CoA binding first followed by histamine to generate an AANATL7·acetyl-CoA·histamine ternary complex prior to catalysis. Successive pH-activity profiling and site-directed mutagenesis experiments identified two ionizable groups: one with a pKa of 7.1 that is assigned to Glu-26 as a general base and a second pKa of 9.5 that is assigned to the protonation of the thiolate of the coenzyme A product. Using the data generated herein, we propose a chemical mechanism for AANATL7 and define functions for other important amino acid residues involved in substrate binding and regulation of catalysis.
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Affiliation(s)
- Daniel R Dempsey
- †Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Kristen A Jeffries
- †Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Sumit Handa
- †Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Anne-Marie Carpenter
- †Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | | | - David J Merkler
- †Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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13
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Dempsey DR, Jeffries KA, Bond JD, Carpenter AM, Rodriguez-Ospina S, Breydo L, Caswell KK, Merkler DJ. Mechanistic and structural analysis of Drosophila melanogaster arylalkylamine N-acetyltransferases. Biochemistry 2014; 53:7777-93. [PMID: 25406072 PMCID: PMC4270386 DOI: 10.1021/bi5006078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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Arylalkylamine N-acetyltransferase (AANAT) catalyzes the penultimate step in the
biosynthesis of melatonin and other N-acetylarylalkylamides
from the corresponding arylalkylamine and acetyl-CoA. The N-acetylation
of arylalkylamines is a critical step in Drosophila melanogaster for the inactivation of the bioactive amines and the sclerotization
of the cuticle. Two AANAT variants (AANATA and AANATB) have been identified
in D. melanogaster, in which AANATA differs from
AANATB by the truncation of 35 amino acids from the N-terminus. We
have expressed and purified both D. melanogaster AANAT
variants (AANATA and AANATB) in Escherichia coli and
used the purified enzymes to demonstrate that this N-terminal truncation
does not affect the activity of the enzyme. Subsequent characterization
of the kinetic and chemical mechanism of AANATA identified an ordered
sequential mechanism, with acetyl-CoA binding first, followed by tyramine.
We used a combination of pH–activity profiling and site-directed
mutagenesis to study prospective residues believed to function in
AANATA catalysis. These data led to an assignment of Glu-47 as the
general base in catalysis with an apparent pKa of 7.0. Using the data generated for the kinetic mechanism,
structure–function relationships, pH–rate profiles,
and site-directed mutagenesis, we propose a chemical mechanism for
AANATA.
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Affiliation(s)
- Daniel R Dempsey
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
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14
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Srivastava P, Khandokar YB, Swarbrick CMD, Roman N, Himiari Z, Sarker S, Raidal SR, Forwood JK. Structural characterization of a Gcn5-related N-acetyltransferase from Staphylococcus aureus. PLoS One 2014; 9:e102348. [PMID: 25118709 PMCID: PMC4131848 DOI: 10.1371/journal.pone.0102348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/18/2014] [Indexed: 11/19/2022] Open
Abstract
The Gcn5-related N-acetyltransferases (GNATs) are ubiquitously expressed in nature and perform a diverse range of cellular functions through the acetylation of small molecules and protein substrates. Using activated acetyl coenzyme A as a common acetyl donor, GNATs catalyse the transfer of an acetyl group to acceptor molecules including aminoglycoside antibiotics, glucosamine-6-phosphate, histones, serotonin and spermidine. There is often only very limited sequence conservation between members of the GNAT superfamily, in part, reflecting their capacity to bind a diverse array of substrates. In contrast, the secondary and tertiary structures are highly conserved, but then at the quaternary level there is further diversity, with GNATs shown to exist in monomeric, dimeric, or tetrameric states. Here we describe the X-ray crystallographic structure of a GNAT enzyme from Staphylococcus aureus with only low sequence identity to previously solved GNAT proteins. It contains many of the classical GNAT motifs, but lacks other hallmarks of the GNAT fold including the classic β-bulge splayed at the β-sheet interface. The protein is likely to be a dimer in solution based on analysis of the asymmetric unit within the crystal structure, homology with related GNAT family members, and size exclusion chromatography. The study provides the first high resolution structure of this enzyme, providing a strong platform for substrate and cofactor modelling, and structural/functional comparisons within this diverse enzyme superfamily.
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Affiliation(s)
- Parul Srivastava
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Yogesh B. Khandokar
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Crystall M. D. Swarbrick
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Zainab Himiari
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Subir Sarker
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- * E-mail:
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15
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Vavricka CJ, Han Q, Mehere P, Ding H, Christensen BM, Li J. Tyrosine metabolic enzymes from insects and mammals: a comparative perspective. INSECT SCIENCE 2014; 21:13-19. [PMID: 23955993 DOI: 10.1111/1744-7917.12038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/17/2013] [Indexed: 06/02/2023]
Abstract
Differences in the metabolism of tyrosine between insects and mammals present an interesting example of molecular evolution. Both insects and mammals possess fine-tuned systems of enzymes to meet their specific demands for tyrosine metabolites; however, more homologous enzymes involved in tyrosine metabolism have emerged in many insect species. Without knowledge of modern genomics, one might suppose that mammals, which are generally more complex than insects and require tyrosine as a precursor for important catecholamine neurotransmitters and for melanin, should possess more enzymes to control tyrosine metabolism. Therefore, the question of why insects actually possess more tyrosine metabolic enzymes is quite interesting. It has long been known that insects rely heavily on tyrosine metabolism for cuticle hardening and for innate immune responses, and these evolutionary constraints are likely the key answers to this question. In terms of melanogenesis, mammals also possess a high level of regulation; yet mammalian systems possess more mechanisms for detoxification whereas insects accelerate pathways like melanogenesis and therefore must bear increased oxidative pressure. Our research group has had the opportunity to characterize the structure and function of many key proteins involved in tyrosine metabolism from both insects and mammals. In this mini review we will give a brief overview of our research on tyrosine metabolic enzymes in the scope of an evolutionary perspective of mammals in comparison to insects.
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Affiliation(s)
- Christopher John Vavricka
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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16
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Zhang JL, Zheng QC, Li ZQ, Zhang HX. Theoretical evaluation and improvement on the potency of the rhodanine-based inhibitors for human serotoninN-acetyltransferase. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.854894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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He Y, Roth C, Turkenburg JP, Davies GJ. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:186-95. [PMID: 24419391 PMCID: PMC3919268 DOI: 10.1107/s1399004713029155] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/22/2013] [Indexed: 12/01/2022]
Abstract
The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP_05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.
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Affiliation(s)
- Yuan He
- College of Chemistry and Materials Science, Northwest University, Xi’an 710069, People’s Republic of China
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Christian Roth
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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18
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Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya. Proc Natl Acad Sci U S A 2013; 111:314-9. [PMID: 24351931 DOI: 10.1073/pnas.1312634110] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Melatonin (N-acetyl-5-methoxytrypamine) is the vertebrate hormone of the night: circulating levels at night are markedly higher than day levels. This increase is driven by precisely regulated increases in acetylation of serotonin in the pineal gland by arylalkylamine N-acetyltransferase (AANAT), the penultimate enzyme in the synthesis of melatonin. This unique essential role of AANAT in vertebrate timekeeping is recognized by the moniker the timezyme. AANAT is also found in the retina, where melatonin is thought to play a paracrine role. Here, we focused on the evolution of AANAT in early vertebrates. AANATs from Agnathans (lamprey) and Chondrichthyes (catshark and elephant shark) were cloned, and it was found that pineal glands and retinas from these groups express a form of AANAT that is compositionally, biochemically, and kinetically similar to AANATs found in bony vertebrates (VT-AANAT). Examination of the available genomes indicates that VT-AANAT is absent from other forms of life, including the Cephalochordate amphioxus. Phylogenetic analysis and evolutionary rate estimation indicate that VT-AANAT evolved from the nonvertebrate form of AANAT after the Cephalochordate-Vertebrate split over one-half billion years ago. The emergence of VT-AANAT apparently involved a dramatic acceleration of evolution that accompanied neofunctionalization after a duplication of the nonvertebrate AANAT gene. This scenario is consistent with the hypotheses that the advent of VT-AANAT contributed to the evolution of the pineal gland and lateral eyes from a common ancestral photodetector and that it was not a posthoc recruitment.
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19
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Cazaméa-Catalan D, Magnanou E, Helland R, Besseau L, Boeuf G, Falcón J, Jørgensen EH. Unique arylalkylamine N-acetyltransferase-2 polymorphism in Salmonids and profound variations in thermal stability and catalytic efficiency conferred by two residues. J Exp Biol 2013; 216:1938-48. [DOI: 10.1242/jeb.080960] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Summary
Melatonin contributes to synchronizing major biological and behavioral functions to the cyclic changes in the environment. The arylalkylamine N-acetyltransferase (AANAT) is responsible for a daily rhythm in melatonin secretion. Teleost possess two enzyme forms, AANAT1 and AANAT2, preferentially expressed in the retina and pineal organ, respectively. The concomitant action of light and temperature shapes the daily and seasonal changes in melatonin secretion: the former controls duration while the latter modulates amplitude. Investigating the respective roles of light and temperature is particularly relevant in the context of a global warming likely to affect the way fish decode and anticipate seasonal changes with dramatic consequences on their physiology and behavior. Here we investigated the impact of temperature on pineal melatonin secretion of a migratory species, the Arctic charr (Salvelinus alpinus), the northernmost living and cold adapted salmonid. We show that temperature impacts directly melatonin production in cultured pineal organs. We also show that one organ expresses two AANAT2 transcripts displaying high similarity between them and with trout Oncorhynchus mykiss AANAT2, differing by only two amino acid sites. We compared the kinetics and 3D models of these enzymes as well as of a chimeric construct, particularly with regard to their response to temperature. Our study brings interesting and totally new information on the evolutionary diversity of AANAT enzymes in Teleost and on the role played by specific residues in the catalytic properties of the enzymes.
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Affiliation(s)
| | | | | | | | | | - Jack Falcón
- CNRS, Biologie Intégrative des Organismes Marins
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20
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Zhao G, Allewell NM, Tuchman M, Shi D. Structure of the complex of Neisseria gonorrhoeae N-acetyl-L-glutamate synthase with a bound bisubstrate analog. Biochem Biophys Res Commun 2012; 430:1253-8. [PMID: 23261468 DOI: 10.1016/j.bbrc.2012.12.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
Abstract
N-Acetyl-L-glutamate synthase catalyzes the conversion of AcCoA and glutamate to CoA and N-acetyl-L-glutamate (NAG), the first step of the arginine biosynthetic pathway in lower organisms. In mammals, NAG is an obligate cofactor of carbamoyl phosphate synthetase I in the urea cycle. We have previously reported the structures of NAGS from Neisseria gonorrhoeae (ngNAGS) with various substrates bound. Here we reported the preparation of the bisubstrate analog, CoA-S-acetyl-L-glutamate, the crystal structure of ngNAGS with CoA-NAG bound, and kinetic studies of several active site mutants. The results are consistent with a one-step nucleophilic addition-elimination mechanism with Glu353 as the catalytic base and Ser392 as the catalytic acid. The structure of the ngNAGS-bisubstrate complex together with the previous ngNAGS structures delineates the catalytic reaction path for ngNAGS.
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Affiliation(s)
- Gengxiang Zhao
- Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children's National Medical Center, The George Washington University, Washington, DC 20010, USA
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21
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Cazaméa-Catalan D, Magnanou E, Helland R, Vanegas G, Besseau L, Boeuf G, Paulin CH, Jørgensen EH, Falcón J. Functional diversity of Teleost arylalkylamineN-acetyltransferase-2: is thetimezymeevolution driven by habitat temperature? Mol Ecol 2012; 21:5027-41. [DOI: 10.1111/j.1365-294x.2012.05725.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/21/2012] [Accepted: 06/28/2012] [Indexed: 01/19/2023]
Affiliation(s)
| | | | - R. Helland
- Norstruct; Department of Chemistry; Faculty of Science and Technology; University of Tromsø; N-9037; Tromsø; Norway
| | - G. Vanegas
- Cátedra de Fisiología Normal; Escuela de Medicina “José María Vargas”; Facultad de Medicina; Universidad Central de Venezuela; Caracas; Venezuela
| | | | | | | | - E. H. Jørgensen
- Department of Arctic and Marine Biology; Faculty of Biosciences; Fisheries and Economy; University of Tromsø; N-9037; Tromsø; Norway
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22
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Pflug A, Johnson KA, Engh RA. Anomalous dispersion analysis of inhibitor flexibility: a case study of the kinase inhibitor H-89. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:873-7. [PMID: 22869112 PMCID: PMC3412763 DOI: 10.1107/s1744309112028655] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/24/2012] [Indexed: 11/10/2022]
Abstract
With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply. Discrepancies between the modelled crystal structure and the physiological range of structures generally prevent quantitative estimation of binding energies. Improved crystal structure resolution will often not aid energy estimation because the conditions which provide the highest rigidity and resolution are not likely to reflect physiological conditions. Instead, strategies must be employed to measure and model flexibility and multiple binding modes to supplement crystallographic information. One useful tool is the use of anomalous dispersion for small molecules that contain suitable atoms. Here, an analysis of the binding of the kinase inhibitor H-89 to protein kinase A (PKA) is presented. H-89 contains a bromobenzene moiety that apparently binds with multiple conformations in the kinase ATP pocket. Using anomalous dispersion methods, it was possible to resolve these conformations into two distinct binding geometries.
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Affiliation(s)
- Alexander Pflug
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Kenneth A. Johnson
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Richard A. Engh
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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23
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Evolution of insect arylalkylamine N-acetyltransferases: structural evidence from the yellow fever mosquito, Aedes aegypti. Proc Natl Acad Sci U S A 2012; 109:11669-74. [PMID: 22753468 DOI: 10.1073/pnas.1206828109] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Arylalkylamine N-acetyltransferase (aaNAT) catalyzes the transacetylation from acetyl-CoA to arylalkylamines. aaNATs are involved in sclerotization and neurotransmitter inactivation in insects. Phyletic distribution analysis confirms three clusters of aaNAT-like sequences in insects: typical insect aaNAT, polyamine NAT-like aaNAT, and mosquito unique putative aaNAT (paaNAT). Here we studied three proteins: aaNAT2, aaNAT5b, and paaNAT7, each from a different cluster. aaNAT2, a protein from the typical insect aaNAT cluster, uses histamine as a substrate as well as the previously identified arylalkylamines. aaNAT5b, a protein from polyamine NAT -like aaNAT cluster, uses hydrazine and histamine as substrates. The crystal structure of aaNAT2 was determined using single-wavelength anomalous dispersion methods, and that of native aaNAT2, aaNAT5b and paaNAT7 was detected using molecular replacement techniques. All three aaNAT structures have a common fold core of GCN5-related N-acetyltransferase superfamily proteins, along with a unique structural feature: helix/helices between β3 and β4 strands. Our data provide a start toward a more comprehensive understanding of the structure-function relationship and physiology of aaNATs from the mosquito Aedes aegypti and serve as a reference for studying the aaNAT family of proteins from other insect species. The structures of three different types of aaNATs may provide targets for designing insecticides for use in mosquito control.
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24
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Zilberman-Peled B, Bransburg-Zabary S, Klein DC, Gothilf Y. Molecular evolution of multiple arylalkylamine N-acetyltransferase (AANAT) in fish. Mar Drugs 2011; 9:906-921. [PMID: 21673898 PMCID: PMC3111191 DOI: 10.3390/md9050906] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/16/2011] [Accepted: 05/17/2011] [Indexed: 11/26/2022] Open
Abstract
Arylalkylamine N-acetyltransferase (AANAT) catalyzes the transfer of an acetyl group from acetyl coenzyme A (AcCoA) to arylalkylamines, including indolethylamines and phenylethylamines. Multiple aanats are present in teleost fish as a result of whole genome and gene duplications. Fish aanat1a and aanat2 paralogs display different patterns of tissue expression and encode proteins with different substrate preference: AANAT1a is expressed in the retina, and acetylates both indolethylamines and phenylethylamines; while AANAT2 is expressed in the pineal gland, and preferentially acetylates indolethylamines. The two enzymes are therefore thought to serve different roles. Here, the molecular changes that led to their specialization were studied by investigating the structure-function relationships of AANATs in the gilthead seabream (sb, Sperus aurata). Acetylation activity of reciprocal mutated enzymes pointed to specific residues that contribute to substrate specificity of the enzymes. Inhibition tests followed by complementary analyses of the predicted three-dimensional models of the enzymes, suggested that both phenylethylamines and indolethylamines bind to the catalytic pocket of both enzymes. These results suggest that substrate selectivity of AANAT1a and AANAT2 is determined by the positioning of the substrate within the catalytic pocket, and its accessibility to catalysis. This illustrates the evolutionary process by which enzymes encoded by duplicated genes acquire different activities and play different biological roles.
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Affiliation(s)
- Bina Zilberman-Peled
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +972-3-6409041; Fax: +972-3-6406329
| | - Sharron Bransburg-Zabary
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel; E-Mail:
| | - David C. Klein
- Section on Neuroendocrinology, Office of the Scientific Directory, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; E-Mail:
| | - Yoav Gothilf
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel; E-Mail:
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25
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Characterization, localization, essentiality, and high-resolution crystal structure of glucosamine 6-phosphate N-acetyltransferase from Trypanosoma brucei. EUKARYOTIC CELL 2011; 10:985-97. [PMID: 21531872 DOI: 10.1128/ec.05025-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A gene predicted to encode Trypanosoma brucei glucosamine 6-phosphate N-acetyltransferase (TbGNA1; EC 2.3.1.4) was cloned and expressed in Escherichia coli. The recombinant protein was enzymatically active, and its high-resolution crystal structure was obtained at 1.86 Å. Endogenous TbGNA1 protein was localized to the peroxisome-like microbody, the glycosome. A bloodstream-form T. brucei GNA1 conditional null mutant was constructed and shown to be unable to sustain growth in vitro under nonpermissive conditions, demonstrating that there are no metabolic or nutritional routes to UDP-GlcNAc other than via GlcNAc-6-phosphate. Analysis of the protein glycosylation phenotype of the TbGNA1 mutant under nonpermissive conditions revealed that poly-N-acetyllactosamine structures were greatly reduced in the parasite and that the glycosylation profile of the principal parasite surface coat component, the variant surface glycoprotein (VSG), was modified. The significance of results and the potential of TbGNA1 as a novel drug target for African sleeping sickness are discussed.
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Iqbal A, Arunlanantham H, Brown T, Chowdhury R, Clifton IJ, Kershaw NJ, Hewitson KS, McDonough MA, Schofield CJ. Crystallographic and mass spectrometric analyses of a tandem GNAT protein from the clavulanic acid biosynthesis pathway. Proteins 2010; 78:1398-407. [PMID: 20014241 DOI: 10.1002/prot.22653] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
(3R,5R)-Clavulanic acid (CA) is a clinically important inhibitor of Class A beta-lactamases. Sequence comparisons suggest that orf14 of the clavulanic acid biosynthesis gene cluster encodes for an acetyl transferase (CBG). Crystallographic studies reveal CBG to be a member of the emerging structural subfamily of tandem Gcn5-related acetyl transferase (GNAT) proteins. Two crystal forms (C2 and P2(1) space groups) of CBG were obtained; in both forms one molecule of acetyl-CoA (AcCoA) was bound to the N-terminal GNAT domain, with the C-terminal domain being unoccupied by a ligand. Mass spectrometric analyzes on CBG demonstrate that, in addition to one strongly bound AcCoA molecule, a second acyl-CoA molecule can bind to CBG. Succinyl-CoA and myristoyl-CoA displayed the strongest binding to the "second" CoA binding site, which is likely in the C-terminal GNAT domain. Analysis of the CBG structures, together with those of other tandem GNAT proteins, suggest that the AcCoA in the N-terminal GNAT domain plays a structural role whereas the C-terminal domain is more likely to be directly involved in acetyl transfer. The available crystallographic and mass spectrometric evidence suggests that binding of the second acyl-CoA occurs preferentially to monomeric rather than dimeric CBG. The N-terminal AcCoA binding site and the proposed C-terminal acyl-CoA binding site of CBG are compared with acyl-CoA binding sites of other tandem and single domain GNAT proteins.
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Iinoya K, Kotani T, Sasano Y, Takagi H. Engineering of the yeast antioxidant enzyme Mpr1 for enhanced activity and stability. Biotechnol Bioeng 2009; 103:341-52. [PMID: 19170243 DOI: 10.1002/bit.22247] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The budding yeast Saccharomyces cerevisiae Sigma1278b has the MPR1 gene, which confers resistance to the proline analogue azetidine-2-carboxylate (AZC). This gene encodes an N-acetyltransferase Mpr1 that detoxifies AZC, and the homologous genes have been found in many yeasts. Recently, we found that Mpr1 protects yeast cells by reducing the intracellular reactive oxygen species (ROS) levels under oxidative stresses, such as heat-shock, freezing, or ethanol treatment. Unlike the known antioxidant enzymes, Mpr1 is thought to acetylate toxic metabolite(s) involved in ROS generation via oxidative events. To improve the enzymatic functions of Mpr1, we applied PCR random mutagenesis to MPR1. The mutagenized plasmid library was introduced into the S. cerevisiae S288C strain lacking MPR1, and we successfully isolated two Mpr1 variants with higher AZC resistance (K63R and F65L/L117V). Interestingly, overexpression of the K63R variant was found to increase cell viability or decrease intracellular ROS levels after exposure to H(2)O(2) or ethanol compared with the wild-type Mpr1. In vitro studies with the recombinant enzymes showed that the catalytic efficiency of the K63R variant for AZC and acetyl-CoA was higher than that of the wild-type Mpr1 and that the F65L mutation greatly enhanced the thermal stability. The mutational analysis and molecular modeling suggest that an alpha-helix containing Lys63 and Phe65 has important roles in the function of Mpr1. In addition, the wild-type and K63R variant Mpr1 reduced intracellular ROS levels under ethanol stress conditions on haploid sake yeast cells. These results suggest that engineering Mpr1 might be useful in breeding oxidative stress-tolerant yeast strains.
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Affiliation(s)
- Kaoru Iinoya
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Okazaki M, Higuchi K, Hanawa Y, Shiraiwa Y, Ezura H. Cloning and characterization of a Chlamydomonas reinhardtii cDNA arylalkylamine N-acetyltransferase and its use in the genetic engineering of melatonin content in the Micro-Tom tomato. J Pineal Res 2009; 46:373-82. [PMID: 19552760 DOI: 10.1111/j.1600-079x.2009.00673.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Melatonin is found in a wide variety of plant species. Several investigators have studied the physiological roles of melatonin in plants. However, its role is not well understood because of the limited information on its biosynthetic pathway. To clarify melatonin biosynthesis in plants, we isolated a cDNA-coded arylalkylamine N-acetyltransferase (AANAT), a possible limiting enzyme for melatonin biosynthesis, from Chlamydomonas reinhardtii (designated as CrAANAT). The predicted amino acid sequence of CrAANAT shares 39.0% homology to AANAT from Ostreococcus tauri and lacks cAMP-dependent protein kinase phosphorylation sites in the N- and C-terminal regions that are conserved in vertebrates. The enzyme activity of CrAANAT was confirmed by in vitro assay using Escherichia coli. Transgenic plants constitutively expressing the CrAANAT were produced using Micro-Tom, a model cultivar of tomato (Solanum lycopersicum L.). The transgenic Micro-Tom exhibited higher melatonin content compared with wild type, suggesting that melatonin was synthesized from serotonin via N-acetylserotonin in plants. Moreover, the melatonin-rich transgenic Micro-Tom can be used to elucidate the role of melatonin in plant development.
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Affiliation(s)
- Masateru Okazaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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29
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Structural and kinetic differences between human and Aspergillus fumigatus D-glucosamine-6-phosphate N-acetyltransferase. Biochem J 2009; 415:217-23. [PMID: 18601654 DOI: 10.1042/bj20081000] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aspergillus fumigatus is the causative agent of aspergillosis, a frequently invasive colonization of the lungs of immunocompromised patients. GNA1 (D-glucosamine-6-phosphate N-acetyltransferase) catalyses the acetylation of GlcN-6P (glucosamine-6-phosphate) to GlcNAc-6P (N-acetylglucosamine-6-phosphate), a key intermediate in the UDP-GlcNAc biosynthetic pathway. Gene disruption of gna1 in yeast and Candida albicans has provided genetic validation of the enzyme as a potential target. An understanding of potential active site differences between the human and A. fumigatus enzymes is required to enable further work aimed at identifying selective inhibitors for the fungal enzyme. In the present study, we describe crystal structures of both human and A. fumigatus GNA1, as well as their kinetic characterization. The structures show significant differences in the sugar-binding site with, in particular, several non-conservative substitutions near the phosphate-binding pocket. Mutagenesis targeting these differences revealed drastic effects on steady-state kinetics, suggesting that the differences could be exploitable with small-molecule inhibitors.
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30
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Vetting MW, Bareich DC, Yu M, Blanchard JS. Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-acetylation of ribosomal protein S18. Protein Sci 2008; 17:1781-90. [PMID: 18596200 DOI: 10.1110/ps.035899.108] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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31
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Pavlicek J, Coon SL, Ganguly S, Weller JL, Hassan SA, Sackett DL, Klein DC. Evidence that proline focuses movement of the floppy loop of arylalkylamine N-acetyltransferase (EC 2.3.1.87). J Biol Chem 2008; 283:14552-8. [PMID: 18362150 PMCID: PMC2386931 DOI: 10.1074/jbc.m800593200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/14/2008] [Indexed: 11/06/2022] Open
Abstract
Arylalkylamine N-acetyltransferase (AANAT) catalyzes the N-acetylation of serotonin, the penultimate step in the synthesis of melatonin. Pineal AANAT activity increases at night in all vertebrates, resulting in increased melatonin production. This increases circulating levels of melatonin, thereby providing a hormonal signal of darkness. Kinetic and structural analysis of AANAT has determined that one element is floppy. This element, termed Loop 1, is one of three loops that comprise the arylalkylamine binding pocket. During the course of chordate evolution, Loop 1 acquired the tripeptide CPL, and the enzyme became highly active. Here we focused on the functional importance of the CPL tripeptide and found that activity was markedly reduced when it was absent. Moreover, increasing the local flexibility of this tripeptide region by P64G and P64A mutations had the counterintuitive effect of reducing activity and reducing the overall movement of Loop 1, as estimated from Langevin dynamics simulations. Binding studies indicate that these mutations increased the off-rate constant of a model substrate without altering the dissociation constant. The structural kink and local rigidity imposed by Pro-64 may enhance activity by favoring configurations of Loop 1 that facilitate catalysis and do not become immobilized by intramolecular interactions.
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Affiliation(s)
- Jiri Pavlicek
- Section of Neuroendocrinology, Program on Developmental Endocrinology and Genetics, NIH, Bethesda, MD 20892, USA
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Kotani T, Takagi H. Identification of amino acid residues essential for the yeast N-acetyltransferase Mpr1 activity by site-directed mutagenesis. FEMS Yeast Res 2008; 8:607-14. [PMID: 18373682 DOI: 10.1111/j.1567-1364.2008.00374.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We previously discovered that the budding yeast Saccharomyces cerevisiae Sigma1278b has the MPR1 gene that confers resistance to the proline analogue azetidine-2-carboxylate (AZC). The MPR1-encoded protein (Mpr1) is an N-acetyltransferase that detoxifies AZC and is a novel member of the GCN5-related N-acetyltransferase (GNAT) superfamily. Mpr1 can reduce intracellular oxidation levels and protect yeast cells from oxidative stress, heat shock, freezing, or ethanol treatment. Here, we analyzed the amino acid residues in Mpr1 involved in substrate binding and catalysis by site-directed mutagenesis. The mutated genes were expressed in Escherichia coli, and the recombinant Strep-tagged fusion proteins were analyzed in terms of AZC resistance and acetyltransferase activity. The replacement of Arg145, which is conserved in the GNAT superfamily, by Ala, Asp, Glu, Gly, or Trp led to a growth defect of transformants grown in the presence of AZC. Kinetic studies demonstrated that these mutations caused a large reduction in the affinity for AZC and acetyl-CoA, suggesting that Arg145 interacts with both substrates. Among seven conserved Tyr residues, one of which may be a catalytic residue in the GNAT superfamily, Tyr166Ala- showed no detectable activity and Tyr166Phe-Mpr1, a remarkable decrease of the k(cat)/K(m) value. This result suggests that Tyr166 is critical for the catalysis.
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Affiliation(s)
- Tetsuya Kotani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
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Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA. De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem 2007; 50:5330-8. [PMID: 17924613 DOI: 10.1021/jm0706463] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AANAT) is a member of the GCN5 N-acetyltransferase (GNAT) superfamily and catalyzes the penultimate step in the biosynthesis of melatonin; a large daily rhythm in AANAT activity drives the daily rhythm in circulating melatonin. We have used a structure-based computational approach to identify the first druglike and selective inhibitors of AANAT. Approximately 1.2 million compounds were virtually screened by 3D high-throughput docking into the active site of X-ray structures for AANAT, and in total 241 compounds were tested as inhibitors. One compound class, containing a rhodanine scaffold, exhibited low micromolar competitive inhibition against acetyl-CoA (AcCoA) and proved to be effective in blocking melatonin production in pineal cells. Compounds from this class are predicted to bind as bisubstrate inhibitors through interactions with the AcCoA and serotonin binding sites. Overall, this study demonstrates the feasibility of using virtual screening to identify small molecules that are selective inhibitors of AANAT.
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Affiliation(s)
- Lawrence M Szewczuk
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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Abstract
Arylalkylamine N-acetyltransferase controls daily changes in melatonin production by the pineal gland and thereby plays a unique role in biological timing in vertebrates. Arylalkylamine N-acetyltransferase is also expressed in the retina, where it may play other roles in addition to signaling, including neurotransmission and detoxification. Large changes in activity reflect cyclic 3',5'-adenosine monophosphate-dependent phosphorylation of arylalkylamine N-acetyltransferase, leading to formation of a regulatory complex with 14-3-3 proteins. This activates the enzyme and prevents proteosomal proteolysis. The conserved features of regulatory systems that control arylalkylamine N-acetyltransferase are a circadian clock and environmental lighting.
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Affiliation(s)
- David C Klein
- Section on Neuroendocrinology, Office of Scientific Director, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA.
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35
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Hung MN, Rangarajan E, Munger C, Nadeau G, Sulea T, Matte A. Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. J Bacteriol 2006; 188:5606-17. [PMID: 16855251 PMCID: PMC1540030 DOI: 10.1128/jb.00306-06] [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] [Received: 03/01/2006] [Accepted: 05/22/2006] [Indexed: 11/20/2022] Open
Abstract
Enterobacterial common antigen (ECA) is a polysaccharide found on the outer membrane of virtually all gram-negative enteric bacteria and consists of three sugars, N-acetyl-d-glucosamine, N-acetyl-d-mannosaminuronic acid, and 4-acetamido-4,6-dideoxy-d-galactose, organized into trisaccharide repeating units having the sequence -->3)-alpha-d-Fuc4NAc-(1-->4)-beta-d-ManNAcA-(1-->4)-alpha-d-GlcNAc-(1-->. While the precise function of ECA is unknown, it has been linked to the resistance of Shiga-toxin-producing Escherichia coli (STEC) O157:H7 to organic acids and the resistance of Salmonella enterica to bile salts. The final step in the synthesis of 4-acetamido-4,6-dideoxy-d-galactose, the acetyl-coenzyme A (CoA)-dependent acetylation of the 4-amino group, is carried out by TDP-fucosamine acetyltransferase (WecD). We have determined the crystal structure of WecD in apo form at a 1.95-Angstrom resolution and bound to acetyl-CoA at a 1.66-Angstrom resolution. WecD is a dimeric enzyme, with each monomer adopting the GNAT N-acetyltransferase fold, common to a number of enzymes involved in acetylation of histones, aminoglycoside antibiotics, serotonin, and sugars. The crystal structure of WecD, however, represents the first structure of a GNAT family member that acts on nucleotide sugars. Based on this cocrystal structure, we have used flexible docking to generate a WecD-bound model of the acetyl-CoA-TDP-fucosamine tetrahedral intermediate, representing the structure during acetyl transfer. Our structural data show that WecD does not possess a residue that directly functions as a catalytic base, although Tyr208 is well positioned to function as a general acid by protonating the thiolate anion of coenzyme A.
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Affiliation(s)
- Ming-Ni Hung
- Biotechnology Research Institute, 6100 Royalmount Ave., Montreal QC, Canada H4P 2R2
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36
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Gao F, Yan X, Baettig OM, Berghuis AM, Auclair K. Regio- and chemoselective 6'-N-derivatization of aminoglycosides: bisubstrate inhibitors as probes to study aminoglycoside 6'-N-acetyltransferases. Angew Chem Int Ed Engl 2006; 44:6859-62. [PMID: 16206301 DOI: 10.1002/anie.200501399] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Feng Gao
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 2K6, Canada
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Toleman CA, Paterson AJ, Kudlow JE. The histone acetyltransferase NCOAT contains a zinc finger-like motif involved in substrate recognition. J Biol Chem 2005; 281:3918-25. [PMID: 16356930 DOI: 10.1074/jbc.m510485200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear cytoplasmic O-GlcNAcase and acetyltransferase (NCOAT) is a bifunctional enzyme with both glycoside hydrolase and alkyltransferase activity. Its O-GlcNAcase active site lies in the N terminus of the enzyme and its histone acetyltransferase (HAT) domain lies in the C terminus. Whereas the HAT domain of the enzyme is catalytically and structurally similar to other acetyltransferases across subfamilies, NCOAT has a motif resembling a zinc finger-like domain unique to the MYST family of HATs. Among the MYST family, this zinc finger, or zinc finger-like domain, is responsible for making contacts with the histone tails within nucleosomes for the HAT to catalyze its respective reaction. Here, we show that NCOAT has the ability to directly associate with both an acetylated and unacetylated histone H4 tail in vitro, and a potential zinc finger-like motif found in NCOAT is implicated in this nucleosomal contact, and is necessary for fully efficient enzymatic activity. Subsequent to the catalysis of acetyltransfer to lysine 8 of histone H4 for the enzyme, however, the substrate is released and NCOAT can no longer bind H4 in our assays. Furthermore, this finger domain by itself is sufficient to bind histone H4.
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Affiliation(s)
- Clifford A Toleman
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Alabama, Birmingham, 35294-0012, USA
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Gao F, Yan X, Baettig OM, Berghuis AM, Auclair K. Regio- and Chemoselective 6′-N-Derivatization of Aminoglycosides: Bisubstrate Inhibitors as Probes To Study Aminoglycoside 6′-N-Acetyltransferases. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501399] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Boutin JA, Audinot V, Ferry G, Delagrange P. Molecular tools to study melatonin pathways and actions. Trends Pharmacol Sci 2005; 26:412-9. [PMID: 15992934 DOI: 10.1016/j.tips.2005.06.006] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 05/16/2005] [Accepted: 06/16/2005] [Indexed: 12/15/2022]
Abstract
Melatonin, an indoleamine neurohormone that is synthesized mainly in the pineal gland and derived from 5-HT, has many effects on a wide range of physio-pathological functions. Some of these effects are mediated by the interactions of melatonin with the two melatonin MT1 and MT2 receptors. Other effects are often suggested to be due to the chemical antioxidant nature of this indoleamine, and are observed at high, non-physiological concentrations. However, it is increasingly believed that some of these effects are due to interactions with other protein targets. In this review, we summarize the molecular pharmacology of melatonin, including the main enzymes involved in its synthesis and catabolism, and the proteins that mediate its actions. Furthermore, various compounds, mainly inhibitors and antagonists, that can be used to dissect these functions and pathways are presented.
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Affiliation(s)
- Jean A Boutin
- Pharmacologie Moléculaire et Cellulaire, Institut de Recherches Servier, 125, chemin de Ronde 78290 Croissy-sur-Seine, France.
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40
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Ferry G, Ubeaud C, Dauly C, Mozo J, Guillard S, Berger S, Jimenez S, Scoul C, Leclerc G, Yous S, Delagrange P, Boutin JA. Purification of the recombinant human serotonin N-acetyltransferase (EC 2.3.1.87): further characterization of and comparison with AANAT from other species. Protein Expr Purif 2005; 38:84-98. [PMID: 15477086 DOI: 10.1016/j.pep.2004.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 07/01/2004] [Indexed: 12/01/2022]
Abstract
Melatonin is synthesized by a series of enzymes, the penultimate one, serotonin N-acetyltransferase, catalyzing the limiting reaction. In the present study, we compared the recombinant serotonin N-acetyltransferases from rat, ovine, and human. The human protein is particularly difficult to purify because it interacts strongly with a putative chaperone protein from bacteria whereas the rat and sheep enzymes, which interact less strongly with this protein, have been purified close to homogeneity. We identified the contaminating protein as GroEL, the bacterial equivalent of Hsp60. We present numerous catalytic activities (substrate and cosubstrate specificities as well as inhibitor specificities) measured on the three species enzymes from which we deduced that the presence of the chaperone might partly explain the differences between the various species enzyme characteristics, beside the inter-species ones resulting from sequence differences. Despite several trials reported in the literature, a purification to homogeneity of the human (recombinant) enzyme has never been described. We present a new purification method, by using an original denaturation/renaturation process in which the enzyme is immobilized on an affinity chromatography column. The enzyme is then eluted in an active and pure form (i.e., absence of chaperone). The up-scaled system permitted us to perform the necessary experiments for the measurement of more accurate affinities of human serotonin N-acetyltransferase towards its main natural substrates, showing that only the activity of the enzyme towards phenylethylamine was modified.
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Affiliation(s)
- Gilles Ferry
- Pharmacologie Moléculaire et Cellulaire, Institut de Recherches SERVIER, 125, chemin de Ronde 78290 Croissy-sur-Seine, France
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41
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Vetting MW, S de Carvalho LP, Yu M, Hegde SS, Magnet S, Roderick SL, Blanchard JS. Structure and functions of the GNAT superfamily of acetyltransferases. Arch Biochem Biophys 2005; 433:212-26. [PMID: 15581578 DOI: 10.1016/j.abb.2004.09.003] [Citation(s) in RCA: 463] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 09/02/2004] [Indexed: 11/15/2022]
Abstract
The Gcn5-related N-acetyltransferases are an enormous superfamily of enzymes that are universally distributed in nature and that use acyl-CoAs to acylate their cognate substrates. In this review, we will examine those members of this superfamily that have been both structurally and mechanistically characterized. These include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, protein N-myristoyltransferase, and the Fem family of amino acyl transferases.
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Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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42
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Ferry G, Ubeaud C, Mozo J, Péan C, Hennig P, Rodriguez M, Scoul C, Bonnaud A, Nosjean O, Galizzi JP, Delagrange P, Renard P, Volland JP, Yous S, Lesieur D, Boutin JA. New substrate analogues of human serotonin N-acetyltransferase produce in situ specific and potent inhibitors. ACTA ACUST UNITED AC 2004; 271:418-28. [PMID: 14717709 DOI: 10.1046/j.1432-1033.2003.03942.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Melatonin is synthesized by an enzymatic pathway, in which arylalkylamine (serotonin) N-acetyltransferase catalyzes the rate-limiting step. A previous study reported the discovery of bromoacetyltryptamine (BAT), a new type of inhibitor of this enzyme. This compound is the precursor of a potent bifunctional inhibitor (analogue of the transition state), capable of interfering with both the substrate and the cosubstrate binding sites. This inhibitor is biosynthesized by the enzyme itself in the presence of free coenzyme A. In the present report, we describe the potency of new N-halogenoacetyl derivatives leading to a strong in situ inhibition of serotonin N-acetyltransferase. The new concept behind the mechanism of action of these precursors was studied by following the biosynthesis of the inhibitor from tritiated-BAT in a living cell. The fate of tritiated-phenylethylamine (PEA), a natural substrate of the enzyme, in the presence or absence of [(3)H]BAT was also followed, leading to their incorporation into the reaction product or the inhibitor (N-acetyl[(3)H]PEA and coenzyme A-S[(3)H]acetyltryptamine, respectively). The biosynthesis of this bifunctional inhibitor derived from BAT was also followed by nuclear magnetic resonance during its catalytic production by the pure enzyme. In a similar manner we studied the production of another inhibitor generated from N-[2-(7-hydroxynaphth-1-yl)ethyl]bromoacetamide. New derivatives were also screened for their capacity to inhibit a purified enzyme, in addition to enzyme overexpressed in a cellular model. Some of these compounds proved to be extremely potent, with IC(50)s of approximately 30 nM. As these compounds, by definition, closely resemble the natural substrates of arylalkylamine N-acetyltransferase, we also show that they are potent ligands at the melatonin receptors. Nevertheless, these inhibitors form a series of pharmacological tools that could be used to understand more closely the inhibition of pineal melatonin production in vivo.
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Affiliation(s)
- Gilles Ferry
- Pharmacologie Moléculaire et Cellulaire, Institut de Recherches SERVIER, Croissy-sur-Seine, France
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Shirai H, Mizuguchi K. Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism. FEBS Lett 2003; 555:505-10. [PMID: 14675764 DOI: 10.1016/s0014-5793(03)01314-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Arginine succinyltransferase and succinylarginine dihydrolase catalyze the first two steps of arginine catabolism by the arginine succinyltransferase pathway. This route is the only major arginine catabolic pathway in Escherichia coli including its pathogenic strains O157 and CFT073. We have used fold recognition tools and identified novel homologies between each of these two enzymes and proteins of known three-dimensional structure: arginine succinyltransferase belongs to the acyl-CoA N-acyltransferase superfamily and succinylarginine dihydrolase belongs to the amidinotransferase superfamily. These findings shed light on the structures, catalytic mechanisms and evolution of diverse enzymes involved in arginine catabolism.
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Affiliation(s)
- Hiroki Shirai
- Department of Biochemistry, University of Cambridge, Old Addenbrooks Site, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
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44
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Zheng W, Cole PA. Novel bisubstrate analog inhibitors of serotonin N-acetyltransferase: the importance of being neutral. Bioorg Chem 2003; 31:398-411. [PMID: 12941292 DOI: 10.1016/s0045-2068(03)00081-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Linker modified novel bisubstrate analog inhibitors 4-7 for serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AANAT) have been designed and synthesized. Examination of these inhibitors with AANAT in vitro suggested that: (i) linker hydrogen bonding makes only modest contributions to the affinity of bisubstrate analog inhibitors studied; (ii) greater than or equal to four methylene groups between the indole and the coenzyme A (CoASH) moieties are required for a bisubstrate analog inhibitor to achieve strong AANAT inhibition; (iii) the AANAT active site appears not to accommodate positively charged linkers as well as neutral ones; and (iv) substrate amine pKa depression may constitute one strategy for AANAT substrate recognition and catalysis. The results reported here have enhanced our understanding of AANAT substrate recognition/catalysis, and are important for novel inhibitor design. Since AANAT belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily, our experimental strategies should find applications for other acetyltransferases.
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Affiliation(s)
- Weiping Zheng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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45
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Cebrat M, Kim CM, Thompson PR, Daugherty M, Cole PA. Synthesis and analysis of potential prodrugs of coenzyme A analogues for the inhibition of the histone acetyltransferase p300. Bioorg Med Chem 2003; 11:3307-13. [PMID: 12837541 DOI: 10.1016/s0968-0896(03)00265-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Lys-CoA (1) is a selective inhibitor of p300 histone acetyltransferase (HAT) but shows poor pharmacokinetic properties because of its multiply charged phosphates. In an effort to overcome this limitation, truncated derivatives of 1 were designed, synthesized and tested as p300HAT inhibitors as well as substrates for the CoA biosynthetic bifunctional enzyme phosphopantetheine adenylyltransferase-dephospho-CoA kinase (PPAT/DPCK). Lys-pantetheine (3) and Lys-phosphopantetheine (2) showed no detectable p300HAT inhibition whereas 3'-dephospho-Lys-CoA (5) was a modest p300 inhibitor with IC(50) of 1.6 microM (compared to IC(50) of approximately 50 nM for 1 blocking p300). Compound 2 was shown to be an efficient substrate for PPAT whereas 5 was a very poor DPCK substrate. Further analysis with 3'-dephospho-Me-SCoA (7) indicated that DPCK shows relatively narrow capacity to accept substrates with sulfur substitution. While these results suggest that truncated derivatives of 1 will be of limited value as lead agents for p300 blockade in vivo, they augur well for prodrug versions of CoA analogues that do not require 3'-phosphate substitution for efficient binding to their targets, such as the GCN-5 related N-acetyltransferases.
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Affiliation(s)
- Marek Cebrat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
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46
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Scheibner KA, Zhang Z, Cole PA. Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions. Anal Biochem 2003; 317:226-32. [PMID: 12758261 DOI: 10.1016/s0003-2697(03)00087-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Determination of protein oligomerization state can be technically challenging. We have combined the methods of expressed protein ligation (EPL) and fluorescence resonance energy transfer (FRET) for the analysis of protein homo-oligomerization states. We have attached fluorescein (donor) and rhodamine (acceptor) chromophores via dipeptide linkages to the C-termini of three recombinant proteins and examined the potential for FRET between mixtures of these semisynthetic proteins. The known protein dimer (glutathione S-transferase) showed evidence of FRET and the known protein monomer (SH2 domain phosphatase-1) did not display FRET. Using this method, the previously uncharacterized circadian rhythm enzyme, serotonin N-acetyltransferase, displayed significant FRET, indicating its likely propensity for dimerization or more complex oligomerization. These results establish the potential of the union of EPL and FRET in the analysis of protein-protein interactions and provide insight into the unusual enzymatic behavior of a key circadian rhythm enzyme.
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Affiliation(s)
- Kara A Scheibner
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Rm. 316, Hunterian Bldg., Baltimore, MD 21205, USA
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47
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Boehr DD, Jenkins SI, Wright GD. The molecular basis of the expansive substrate specificity of the antibiotic resistance enzyme aminoglycoside acetyltransferase-6'-aminoglycoside phosphotransferase-2". The role of ASP-99 as an active site base important for acetyl transfer. J Biol Chem 2003; 278:12873-80. [PMID: 12566434 DOI: 10.1074/jbc.m211680200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The most frequent determinant of aminoglycoside antibiotic resistance in Gram-positive bacterial pathogens is a bifunctional enzyme, aminoglycoside acetyltransferase-6'-aminoglycoside phosphotransferase-2" (AAC(6')- aminoglycoside phosphotransferase-2", capable of modifying a wide selection of clinically relevant antibiotics through its acetyltransferase and kinase activities. The aminoglycoside acetyltransferase domain of the enzyme, AAC(6')-Ie, is the only member of the large AAC(6') subclass known to modify fortimicin A and catalyze O-acetylation. We have demonstrated through solvent isotope, pH, and site-directed mutagenesis effects that Asp-99 is responsible for the distinct abilities of AAC(6')-Ie. Moreover, we have demonstrated that small planar molecules such as 1-(bromomethyl)phenanthrene can inactivate the enzyme through covalent modification of this residue. Thus, Asp-99 acts as an active site base in the molecular mechanism of AAC(6')-Ie. The prominent role of this residue in aminoglycoside modification can be exploited as an anchoring site for the development of compounds capable of reversing antibiotic resistance in vivo.
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Affiliation(s)
- David D Boehr
- Antimicrobial Research Centre, Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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Lerner C, Masjost B, Ruf A, Gramlich V, Jakob-Roetne R, Zürcher G, Borroni E, Diederich F. Bisubstrate inhibitors for the enzyme catechol-O-methyltransferase (COMT): influence of inhibitor preorganisation and linker length between the two substrate moieties on binding affinity. Org Biomol Chem 2003; 1:42-9. [PMID: 12929389 DOI: 10.1039/b208690p] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhibition of the enzyme catechol-O-methyltransferase (COMT) is an important approach in the treatment of Parkinson's disease. A series of new potent bisubstrate inhibitors for COMT, resulting from X-ray structure-based design and featuring adenosine and catechol moieties have been synthesised. Biological results show a large dependence of binding affinity on inhibitor preorganisation and the length of the linker between nucleoside and catechol moieties. The most potent bisubstrate inhibitor for COMT has an IC50 value of 9 nM. It exhibits competitive kinetics for the SAM and mixed inhibition kinetics for the catechol binding site. Its bisubstrate binding mode was confirmed by X-ray structure analysis of the ternary complex formed by the inhibitor, COMT and a Mg2+ ion.
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Affiliation(s)
- Christian Lerner
- Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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49
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Qiu W, Campbell RL, Gangloff A, Dupuis P, Boivin RP, Tremblay MR, Poirier D, Lin SX. A concerted, rational design of type 1 17beta-hydroxysteroid dehydrogenase inhibitors: estradiol-adenosine hybrids with high affinity. FASEB J 2002; 16:1829-31. [PMID: 12223444 DOI: 10.1096/fj.02-0026fje] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD type 1) catalyzes the final step in the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. Based on the initial premise to make use of the binding energies of both the substrate and cofactor sites, and molecular modeling starting from the enzyme structure, several estradiol-adenosine hybrids were designed and synthesized. Among these hybrids, EM-1745 with a linker of 8-CH2 groups is proved to be the best competitive inhibitor with a Ki of 3.0 +/- 0.8 nM. The crystal structure of the EM-1745 enzyme complex at 1.6 A provides evidence at atomic resolution of strong interactions between both the steroid and cofactor moieties and the enzyme molecule, as illustrated by a deltaA-weighted 2Fo-Fc electron density map contoured at 3.0 delta. The substrate entry loop is further stabilized in this complex compared with previous complexes of the enzyme. These results confirm our initial strategy of combining studies of structural biology and enzyme mechanism in the inhibitor design, which may be applied to other steroidogenic enzymes involved in human diseases.
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Affiliation(s)
- Wei Qiu
- Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Quebec, G1V 4G2, Canada
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Poux AN, Cebrat M, Kim CM, Cole PA, Marmorstein R. Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Proc Natl Acad Sci U S A 2002; 99:14065-70. [PMID: 12391296 PMCID: PMC137837 DOI: 10.1073/pnas.222373899] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2002] [Indexed: 11/18/2022] Open
Abstract
Histone acetyltransferases (HATs) use acetyl CoA to acetylate target lysine residues within histones and other transcription factors, such as the p53 tumor suppressor, to promote gene activation. HAT enzymes fall into subfamilies with divergence in sequence and substrate preference. Several HAT proteins have been implicated in human cancer. We have previously reported on the preparation of peptide-CoA conjugate inhibitors with distinct specificities for the p300/CBP [cAMP response element binding protein (CREB)-binding protein] or GCN5 HAT subfamilies. Here we report on the crystal structure of the GCN5 HAT bound to a peptide-CoA conjugate containing CoA covalently attached through an isopropionyl linker to Lys-14 of a 20-aa N-terminal fragment of histone H3. Surprisingly, the structure reveals that the H3 portion of the inhibitor is bound outside of the binding site for the histone substrate and that only five of the 20 aa residues of the inhibitor are ordered. Rearrangements within the C-terminal region of the GCN5 protein appear to mediate this peptide displacement. Mutational and enzymatic data support the hypothesis that the observed structure corresponds to a late catalytic intermediate. The structure also provides a structural scaffold for the design of HAT-specific inhibitors that may have therapeutic applications for the treatment of HAT-mediated cancers.
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Affiliation(s)
- Arienne N Poux
- The Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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