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Bisello G, Kusmierska K, Verbeek MM, Sykut-Cegielska J, Willemsen MAAP, Wevers RA, Szymańska K, Poznanski J, Drozak J, Wertheim-Tysarowska K, Rygiel AM, Bertoldi M. The novel P330L pathogenic variant of aromatic amino acid decarboxylase maps on the catalytic flexible loop underlying its crucial role. Cell Mol Life Sci 2022; 79:305. [PMID: 35593933 PMCID: PMC9121088 DOI: 10.1007/s00018-022-04343-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 05/01/2022] [Indexed: 12/14/2022]
Abstract
Aromatic amino acid decarboxylase (AADC) deficiency is a rare monogenic disease, often fatal in the first decade, causing severe intellectual disability, movement disorders and autonomic dysfunction. It is due to mutations in the gene coding for the AADC enzyme responsible for the synthesis of dopamine and serotonin. Using whole exome sequencing, we have identified a novel homozygous c.989C > T (p.Pro330Leu) variant of AADC causing AADC deficiency. Pro330 is part of an essential structural and functional element: the flexible catalytic loop suggested to cover the active site as a lid and properly position the catalytic residues. Our investigations provide evidence that Pro330 concurs in the achievement of an optimal catalytic competence. Through a combination of bioinformatic approaches, dynamic light scattering measurements, limited proteolysis experiments, spectroscopic and in solution analyses, we demonstrate that the substitution of Pro330 with Leu, although not determining gross conformational changes, results in an enzymatic species that is highly affected in catalysis with a decarboxylase catalytic efficiency decreased by 674- and 194-fold for the two aromatic substrates. This defect does not lead to active site structural disassembling, nor to the inability to bind the pyridoxal 5’-phosphate (PLP) cofactor. The molecular basis for the pathogenic effect of this variant is rather due to a mispositioning of the catalytically competent external aldimine intermediate, as corroborated by spectroscopic analyses and pH dependence of the kinetic parameters. Altogether, we determined the structural basis for the severity of the manifestation of AADC deficiency in this patient and discussed the rationale for a precision therapy.
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Affiliation(s)
- Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Katarzyna Kusmierska
- Department of Screening and Metabolic Diagnostics, Institute of Mother and Child, Warsaw, Poland
| | - Marcel M Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Cente, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Paediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Michèl A A P Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Cente, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Krystyna Szymańska
- Department of Child and Adolescent Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | - Jarosław Poznanski
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | | | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy.
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Le NH, Han YH, Ryu SG, Cho J. Mechanistic reaction model for oxidation of sulfur mustard simulant by a catalytic system of nitrate and tribromide. J Hazard Mater 2019; 365:511-518. [PMID: 30466049 DOI: 10.1016/j.jhazmat.2018.11.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
A new metal-free catalytic reaction system is developed to selectively oxidize 2-chloroethyl ethyl sulfide (CEES), a surrogate of sulfur mustard. The combination of two catalytic precursors, tribromide and nitrate, allows a rapid sulfoxidation of CEES even at ambient conditions. The kinetic behaviours at various reaction conditions are investigated to identify the most probable reaction pathways of the development of catalytic loop and the overall reaction steps of CEES sulfoxidation. The mechanistic study demonstrates that the catalytic loop does not require an addition of mineral acid or water, which is common in most other reaction systems. Incomplete catalytic systems with one precursor are also examined to uncover the complex network of sulfoxidation in the catalytic reaction system. The results reveal that the complex between CEES and bromine is a reactive intermediate, bromosulfonium, which can be further catalysed and converted into sulfoxide by nitrate. Based on the proposed reaction mechanism, a predictive kinetic model fully describing most reaction behaviours is developed.
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Affiliation(s)
- Ngan Hong Le
- Research Center for Green Carbon Catalysis, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Department of Advanced Materials and Chemical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Yo-Han Han
- Research Center for Green Carbon Catalysis, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Department of Advanced Materials and Chemical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sam Gon Ryu
- Agency for Defense Development (ADD), Yuseong P.O. Box 35, Daejeon, 34186, Republic of Korea
| | - Joungmo Cho
- Research Center for Green Carbon Catalysis, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea; Department of Advanced Materials and Chemical Engineering, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Kinatukara P, Patel KD, Haque AS, Singh R, Gokhale RS, Sankaranarayananan R. Structural insights into the regulation of NADPH binding to reductase domains of nonribosomal peptide synthetases: A concerted loop movement model. J Struct Biol 2016; 194:368-74. [PMID: 26993465 DOI: 10.1016/j.jsb.2016.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 11/22/2022]
Abstract
The termination module of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) offloads the final product as an acid (occasionally also accompanied by cyclization) upon hydrolysis by employing thioesterase domains (TE-domains). Reductase domains (R-domains) of short-chain dehydrogenase/reductase (SDR) family offer an alternative offloading mechanism by reducing 4'-phosphopantetheine (4'-PPant) arm-tethered peptidyl chain, a thioester, to an aldehyde or an alcohol. Recent studies have highlighted their functional importance, for instance in the glycopeptidolipid (GPL) biosynthesis of Mycobacterium smegmatis, where the resulting alcoholic group is the site for subsequent modifications such as glycosylations. The mechanistic understanding of how these R-domains function in the context of multi-modular NRPS and PKS is poorly understood. In this study, conformational differences in functionally important loops, not reported previously, were identified in a new crystal form of R-domain which may be relevant to functioning in the context of assembly-line NRPS and PKS enzymology. Here, we propose a concerted loop movement model that allows gating of cofactor binding to these enzymes, enabling the release of the final product only after the substrate has reached the active site during biosynthesis, and therefore distinct from a canonical single domain SDR family of enzymes.
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