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Kim S, Chang JH. Structural Analysis of Spermidine Synthase from Kluyveromyces lactis. Molecules 2023; 28:molecules28083446. [PMID: 37110680 PMCID: PMC10146546 DOI: 10.3390/molecules28083446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5'-deoxy-5'-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis (KlSpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species.
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Affiliation(s)
- Seongjin Kim
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Science Education Research Institute, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
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Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis. Catalysts 2022. [DOI: 10.3390/catal12050567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The facultative anaerobic hyperthermophilic crenarchaeon Pyrobaculum calidifontis possesses norspermine (333), norspermidine (33), and spermidine (34) as intracellular polyamines (where the number in parentheses represents the number of methylene CH2 chain units between NH2, or NH). In this study, the polyamine biosynthesis pathway of P. calidifontis was predicted on the basis of the enzymatic properties and crystal structures of an aminopropyltransferase from P. calidifontis (Pc-SpeE). Pc-SpeE shared 75% amino acid identity with the thermospermine synthase from Pyrobaculum aerophilum, and recombinant Pc-SpeE could synthesize both thermospermine (334) and spermine (343) from spermidine and decarboxylated S-adenosyl methionine (dcSAM). Recombinant Pc-SpeE showed high enzymatic activity when aminopropylagmatine and norspermidine were used as substrates. By comparison, Pc-SpeE showed low affinity toward putrescine, and putrescine was not stably bound in its active site. Norspermidine was produced from thermospermine by oxidative degradation using a cell-free extract of P. calidifontis, whereas 1,3-diaminopropane (3) formation was not detected. These results suggest that thermospermine was mainly produced from arginine via agmatine, aminopropylagmatine, and spermidine. Norspermidine was produced from thermospermine by an unknown polyamine oxidase/dehydrogenase followed by norspermine formation by Pc-SpeE.
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Mancheño JM, Atondo E, Tomás-Cortázar J, Luís Lavín J, Plaza-Vinuesa L, Martín-Ruiz I, Barriales D, Palacios A, Daniel Navo C, Sampedro L, Peña-Cearra A, Ángel Pascual-Itoiz M, Castelo J, Carreras-González A, Castellana D, Pellón A, Delgado S, Ruas-Madiedo P, de Las Rivas B, Abecia L, Muñoz R, Jiménez-Osés G, Anguita J, Rodríguez H. A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance. Microb Biotechnol 2020; 15:648-667. [PMID: 33336898 PMCID: PMC8867971 DOI: 10.1111/1751-7915.13732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 11/28/2022] Open
Abstract
Colorectal cancer pathogenesis and progression is associated with the presence of Fusobacterium nucleatum and the reduction of acetylated derivatives of spermidine, as well as dietary components such as tannin-rich foods. We show that a new tannase orthologue of F. nucleatum (TanBFnn ) has significant structural differences with its Lactobacillus plantarum counterpart affecting the flap covering the active site and the accessibility of substrates. Crystallographic and molecular dynamics analysis revealed binding of polyamines to a small cavity that connects the active site with the bulk solvent which interact with catalytically indispensable residues. As a result, spermidine and its derivatives, particularly N8 -acetylated spermidine, inhibit the hydrolytic activity of TanBFnn and increase the toxicity of gallotannins to F. nucleatum. Our results support a model in which the balance between the detoxicant activity of TanBFnn and the presence of metabolic inhibitors can dictate either conducive or unfavourable conditions for the survival of F. nucleatum.
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Affiliation(s)
- José Miguel Mancheño
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano" (IQFR-CSIC), Madrid, 28006, Spain
| | - Estíbaliz Atondo
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Julen Tomás-Cortázar
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain.,UCD Conway Institute, University College of Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - José Luís Lavín
- Bioinformatics Unit, CIC bioGUNE-BRTA, Bizkaia Technology Park, Derio, Bizkaia, 48160, Spain
| | - Laura Plaza-Vinuesa
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28006, Spain
| | - Itziar Martín-Ruiz
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Diego Barriales
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Ainhoa Palacios
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | | | - Leticia Sampedro
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Ainize Peña-Cearra
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain.,Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Leioa, 48940, Spain
| | - Miguel Ángel Pascual-Itoiz
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Janire Castelo
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Ana Carreras-González
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | | | - Aize Pellón
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
| | - Susana Delgado
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Asturias, 33300, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Asturias, 33300, Spain
| | - Blanca de Las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28006, Spain
| | - Leticia Abecia
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain.,Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, Universidad del País Vasco/Euskal Herriko Unibertsitatea, Leioa, 48940, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición (ICTAN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28006, Spain
| | | | - Juan Anguita
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Héctor Rodríguez
- Inflammation and Macrophage Plasticity lab, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Derio, 48160, Spain
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