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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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Witecka A, Kazak V, Kwiatkowski S, Kiersztan A, Jagielski AK, Kozminski W, Augustyniak R, Drozak J. Hydroxysteroid 17-β dehydrogenase 14 (HSD17B14) is an L-fucose dehydrogenase, the initial enzyme of the L-fucose degradation pathway. J Biol Chem 2024:107501. [PMID: 38944119 DOI: 10.1016/j.jbc.2024.107501] [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: 03/29/2024] [Revised: 06/03/2024] [Accepted: 06/15/2024] [Indexed: 07/01/2024] Open
Abstract
L-Fucose (6-deoxy-L-galactose), a monosaccharide abundant in glycolipids and glycoproteins produced by mammalian cells, has been extensively studied for its role in intracellular biosynthesis and recycling of GDP-L-fucose for fucosylation. However, in certain mammalian species, L-fucose is efficiently broken down to pyruvate and lactate in a poorly understood metabolic pathway. In the 1970s, L-fucose dehydrogenase, an enzyme responsible for the initial step of this pathway, was partially purified from pig and rabbit livers and characterized biochemically. However, its molecular identity remained elusive until recently. This study reports the purification, identification, and biochemical characterization of the mammalian L-fucose dehydrogenase. The enzyme was purified from rabbit liver approximately 340-fold. Mass spectrometry analysis of the purified protein preparation identified mammalian hydroxysteroid 17-β dehydrogenase 14 (HSD17B14) as the sole candidate enzyme. Rabbit and human HSD17B14 were expressed in HEK293T and Escherichia coli, respectively, purified and demonstrated to catalyze the oxidation of L-fucose to L-fucono-1,5-lactone, as confirmed by mass spectrometry and NMR analysis. Substrate specificity studies revealed that L-fucose is the preferred substrate for both enzymes. The human enzyme exhibited a catalytic efficiency for L-fucose that was 359-fold higher than its efficiency for estradiol. Additionally, recombinant rat HSD17B14 exhibited negligible activity towards L-fucose, consistent with the absence of L-fucose metabolism in this species. The identification of the gene encoding mammalian L-fucose dehydrogenase provides novel insights into the substrate specificity of enzymes belonging to the 17-β-hydroxysteroid dehydrogenase family. This discovery also paves the way for unraveling the physiological functions of the L-fucose degradation pathway, which remains enigmatic.
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Affiliation(s)
- Apolonia Witecka
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Varvara Kazak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; Celon Pharma S.A., Marymoncka 15, 05-152 Kazun Nowy, Poland
| | - Anna Kiersztan
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Adam K Jagielski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Wiktor Kozminski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Rafal Augustyniak
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland.
| | - Jakub Drozak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Akagashi M, Watanabe S, Kwiatkowski S, Drozak J, Terawaki SI, Watanabe Y. Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates. Sci Rep 2024; 14:14602. [PMID: 38918500 PMCID: PMC11199699 DOI: 10.1038/s41598-024-65627-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
L-2-Keto-3-deoxyfuconate 4-dehydrogenase (L-KDFDH) catalyzes the NAD+-dependent oxidization of L-2-keto-3-deoxyfuconate (L-KDF) to L-2,4-diketo-3-deoxyfuconate (L-2,4-DKDF) in the non-phosphorylating L-fucose pathway from bacteria, and its substrate was previously considered to be the acyclic α-keto form of L-KDF. On the other hand, BDH2, a mammalian homolog with L-KDFDH, functions as a dehydrogenase for cis-4-hydroxy-L-proline (C4LHyp) with the cyclic structure. We found that L-KDFDH and BDH2 utilize C4LHyp and L-KDF, respectively. Therefore, to elucidate unique substrate specificity at the atomic level, we herein investigated for the first time the crystal structures of L-KDFDH from Herbaspirillum huttiense in the ligand-free, L-KDF and L-2,4-DKDF, D-KDP (D-2-keto-3-deoxypentonate; additional substrate), or L-2,4-DKDF and NADH bound forms. In complexed structures, L-KDF, L-2,4-DKDF, and D-KDP commonly bound as a α-furanosyl hemiketal. Furthermore, L-KDFDH showed no activity for L-KDF and D-KDP analogs without the C5 hydroxyl group, which form only the acyclic α-keto form. The C1 carboxyl and α-anomeric C2 hydroxyl groups and O5 oxygen atom of the substrate (and product) were specifically recognized by Arg148, Arg192, and Arg214. The side chain of Trp252 was important for hydrophobically recognizing the C6 methyl group of L-KDF. This is the first example showing the physiological role of the hemiketal of 2-keto-3-deoxysugar acid.
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Affiliation(s)
- Miyu Akagashi
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan.
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan.
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan.
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Shin-Ichi Terawaki
- Division of Structure Analysis of Protein Complex, Proteo-Science Center (PROS), Ehime University, Matsuyama, Ehime, Japan
| | - Yasunori Watanabe
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, Yamagata, 990-8560, Japan
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Deng T, Chen Y, Zhang J, Gao Y, Yang C, Jiang W, Ou X, Wang Y, Guo L, Zhou T, Yuan QS. A Probiotic Bacillus amyloliquefaciens D-1 Strain Is Responsible for Zearalenone Detoxifying in Coix Semen. Toxins (Basel) 2023; 15:674. [PMID: 38133178 PMCID: PMC10747864 DOI: 10.3390/toxins15120674] [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: 10/11/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Zearalenone (ZEN) is a mycotoxin produced by Fusarium spp., which commonly and severely contaminate food/feed. ZEN severely affects food/feed safety and reduces economic losses owing to its carcinogenicity, genotoxicity, reproductive toxicity, endocrine effects, and immunotoxicity. To explore efficient methods to detoxify ZEN, we identified and characterized an efficient ZEN-detoxifying microbiota from the culturable microbiome of Pseudostellaria heterophylla rhizosphere soil, designated Bacillus amyloliquefaciens D-1. Its highest ZEN degradation rate reached 96.13% under the optimal condition. And, D-1 can almost completely remove ZEN (90 μg·g-1) from coix semen in 24 h. Then, the D-1 strain can detoxify ZEN to ZEM, which is a new structural metabolite, through hydrolyzation and decarboxylation at the ester group in the lactone ring and amino acid esterification at C2 and C4 hydroxy. Notably, ZEM has reduced the impact on viability, and the damage of cell membrane and nucleus DNA and can significantly decrease the cell apoptosis in the HepG2 cell and TM4 cell. In addition, it was found that the D-1 strain has no adverse effect on the HepG2 and TM4 cells. Our findings can provide an efficient microbial resource and a reliable reference strategy for the biological detoxification of ZEN.
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Affiliation(s)
- Tao Deng
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Yefei Chen
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Jinqiang Zhang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Yanping Gao
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Changgui Yang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Weike Jiang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Xiaohong Ou
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Yanhong Wang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, China;
| | - Tao Zhou
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
| | - Qing-Song Yuan
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; (T.D.); (J.Z.); (Y.G.); (C.Y.); (W.J.); (Y.W.)
- National Resource Center for Chinese Meteria Medica, State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, China;
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Zhou Y, Wei Y, Jiang L, Zhang Y, Jiao X. A ( S)-3-Hydroxybutyrate Dehydrogenase Belonging to the 3-Hydroxyacyl-CoA Dehydrogenase Family Facilitates Hydroxyacid Degradation in Anaerobic Bacteria. Appl Environ Microbiol 2023; 89:e0036623. [PMID: 37255440 PMCID: PMC10305046 DOI: 10.1128/aem.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Ketone bodies, including acetoacetate, 3-hydroxybutyrate, and acetone, are produced in the liver of animals during glucose starvation. Enzymes for the metabolism of (R)-3-hydroxybutyrate have been extensively studied, but little is known about the metabolism of its enantiomer (S)-3-hydroxybutyrate. Here, we report the characterization of a novel pathway for the degradation of (S)-3-hydroxybutyrate in anaerobic bacteria. We identify and characterize a stereospecific (S)-3-hydroxylbutyrate dehydrogenase (3SHBDH) from Desulfotomaculum ruminis, which catalyzes the reversible NAD(P)H-dependent reduction of acetoacetate to form (S)-3-hydroxybutyrate. 3SHBDH also catalyzes oxidation of d-threonine (2R, 3S) and l-allo-threonine (2S, 3S), consistent with its specificity for β-(3S)-hydroxy acids. Isothermal calorimetry experiments support a sequential mechanism involving binding of NADH prior to (S)-3-hydroxybutyrate. Homologs of 3SHBDH are present in anaerobic fermenting and sulfite-reducing bacteria, and experiments with Clostridium pasteurianum showed that 3SHBDH, acetate CoA-transferase (YdiF), and (S)-3-hydroxybutyryl-CoA dehydrogenase (Hbd) are involved together in the degradation of (S)-3-hydroxybutyrate as a carbon and energy source for growth. (S)-3-hydroxybutyrate is a human metabolic marker and a chiral precursor for chemical synthesis, suggesting potential applications of 3SHBDH in diagnostics or the chemicals industry. IMPORTANCE (R)-3-hydroxybutyrate is well studied as a component of ketone bodies produced by the liver and of bacterial polyesters. However, the biochemistry of its enantiomer (S)-3-hydroxybutyrate is poorly understood. This study describes the identification and characterization of a stereospecific (S)-3-hydroxylbutyrate dehydrogenase and its function in a metabolic pathway for the degradation of (S)-3-hydroxybutyrate as a carbon and energy source in anaerobic bacteria. (S)-3-hydroxybutyrate is a mammalian metabolic marker and a precursor for chemical synthesis and bioplastics, suggesting potential applications of these enzymes in diagnostics and biotechnology.
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Affiliation(s)
- Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality (Ministry of Agriculture of China), Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality (Ministry of Agriculture of China), Yangzhou University, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
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Ogura J, Sato T, Higuchi K, Sivaprakasam S, Kopel J, Bhutia YD, Ganapathy V. Binding of Citrate-Fe 3+ to Plastic Culture Dishes, an Artefact Useful as a Simple Technique to Screen for New Iron Chelators. Int J Mol Sci 2022; 23:ijms23126657. [PMID: 35743100 PMCID: PMC9223814 DOI: 10.3390/ijms23126657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
NaCT mediates citrate uptake in the liver cell line HepG2. When these cells were exposed to iron (Fe3+), citrate uptake/binding as monitored by the association of [14C]-citrate with cells increased. However, there was no change in NaCT expression and function, indicating that NaCT was not responsible for this Fe3+-induced citrate uptake/binding. Interestingly however, the process exhibited substrate selectivity and saturability as if the process was mediated by a transporter. Notwithstanding these features, subsequent studies demonstrated that the iron-induced citrate uptake/binding did not involve citrate entry into cells; instead, the increase was due to the formation of citrate-Fe3+ chelate that adsorbed to the cell surface. Surprisingly, the same phenomenon was observed in culture wells without HepG2 cells, indicating the adsorption of the citrate-Fe3+ chelate to the plastic surface of culture wells. We used this interesting phenomenon as a simple screening technique for new iron chelators with the logic that if another iron chelator is present in the assay system, it would compete with citrate for binding to Fe3+ and prevent the formation and adsorption of citrate-Fe3+ to the culture well. This technique was validated with the known iron chelators deferiprone and deferoxamine, and with the bacterial siderophore 2,3-dihydroxybenzoic acid and the catechol carbidopa.
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Affiliation(s)
- Jiro Ogura
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
- Graduate School of Pharmaceutical Sciences, Yamagata University, Yamagata 990-8560, Japan
| | - Toshihiro Sato
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Kei Higuchi
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
- Department of Pharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Sathish Sivaprakasam
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
| | - Jonathan Kopel
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
| | - Yangzom D. Bhutia
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (J.O.); (T.S.); (K.H.); (S.S.); (J.K.); (Y.D.B.)
- Correspondence: ; Tel.: +1-(806)-743-2518
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