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A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening.

التفاصيل البيبلوغرافية
العنوان: A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening.
المؤلفون: Elisée E; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Ducrot L; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Méheust R; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Bastard K; School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia., Fossey-Jouenne A; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Grogan G; York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK., Pelletier E; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Petit JL; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Stam M; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., de Berardinis V; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Zaparucha A; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France., Vallenet D; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. vallenet@genoscope.cns.fr., Vergne-Vaxelaire C; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. carine.vergne@genoscope.cns.fr.
المصدر: Nature communications [Nat Commun] 2024 Jun 10; Vol. 15 (1), pp. 4933. Date of Electronic Publication: 2024 Jun 10.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Nature Pub. Group
مواضيع طبية MeSH: Amines*/metabolism , Amines*/chemistry, Substrate Specificity ; Oxidoreductases Acting on CH-NH Group Donors/metabolism ; Oxidoreductases Acting on CH-NH Group Donors/genetics ; Oxidoreductases Acting on CH-NH Group Donors/chemistry ; Computational Biology/methods ; Biocatalysis ; Biodiversity ; Models, Molecular
مستخلص: Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.
(© 2024. The Author(s).)
References: Nat Commun. 2019 Aug 16;10(1):3717. (PMID: 31420547)
ChemSusChem. 2022 May 6;15(9):e202102628. (PMID: 35026060)
Curr Opin Chem Biol. 2018 Apr;43:15-22. (PMID: 29100099)
Drug Discov Today Technol. 2010 Winter;7(4):e203-70. (PMID: 24103800)
Front Microbiol. 2018 Feb 14;9:194. (PMID: 29491854)
Sheng Wu Gong Cheng Xue Bao. 2020 Sep 25;36(9):1794-1816. (PMID: 33164457)
ACS Cent Sci. 2021 Jan 27;7(1):55-71. (PMID: 33532569)
Bioinformatics. 2009 Aug 1;25(15):1972-3. (PMID: 19505945)
Bioinformatics. 2012 Dec 1;28(23):3150-2. (PMID: 23060610)
Front Microbiol. 2023 Jan 04;13:1056364. (PMID: 36687660)
Bioinformatics. 2006 Jul 1;22(13):1658-9. (PMID: 16731699)
Bioinformatics. 2005 Apr 1;21(7):951-60. (PMID: 15531603)
Proteins. 2009;77 Suppl 9:114-22. (PMID: 19768677)
Cell Genom. 2022 Apr 28;2(5):100123. (PMID: 36778897)
Chembiochem. 2022 Mar 18;23(6):e202100464. (PMID: 34726813)
Bioinformatics. 2021 Apr 9;37(1):23-28. (PMID: 33416864)
Chembiochem. 2022 May 18;23(10):e202200136. (PMID: 35349204)
BMC Bioinformatics. 2019 Sep 14;20(1):473. (PMID: 31521110)
J Chem Inf Model. 2021 Oct 25;61(10):5293-5303. (PMID: 34528431)
Nucleic Acids Res. 2023 Jan 6;51(D1):D523-D531. (PMID: 36408920)
Nat Biotechnol. 2017 Nov;35(11):1026-1028. (PMID: 29035372)
Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
Nucleic Acids Res. 2023 Jan 6;51(D1):D1373-D1380. (PMID: 36305812)
Angew Chem Int Ed Engl. 2012 Apr 16;51(16):3969-72. (PMID: 22396126)
Chem Soc Rev. 2024 Jan 2;53(1):227-262. (PMID: 38059509)
Nucleic Acids Res. 2020 Jan 8;48(D1):D570-D578. (PMID: 31696235)
Science. 2021 Aug 20;373(6557):871-876. (PMID: 34282049)
Anal Biochem. 1976 May 7;72:248-54. (PMID: 942051)
Nat Biotechnol. 2021 Apr;39(4):499-509. (PMID: 33169036)
J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
Science. 2010 Jul 16;329(5989):305-9. (PMID: 20558668)
Green Chem. 2017 Jan 21;19(2):453-463. (PMID: 28663713)
Nat Commun. 2014 Jun 23;5:4150. (PMID: 24954722)
Nat Commun. 2018 Jan 25;9(1):373. (PMID: 29371626)
Nat Chem. 2017 Oct;9(10):961-969. (PMID: 28937665)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
Traffic. 2016 Nov;17(11):1214-1226. (PMID: 27601190)
Sci Rep. 2023 Jul 21;13(1):11783. (PMID: 37479788)
J Bacteriol. 2009 May;191(9):3162-7. (PMID: 19251850)
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296. (PMID: 33885785)
Science. 2023 Nov 24;382(6673):eadh8615. (PMID: 37995253)
Nat Prod Rep. 2020 Oct 1;37(10):1316-1333. (PMID: 32582886)
Nat Prod Rep. 2021 Nov 17;38(11):1994-2023. (PMID: 34821235)
PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: 22039361)
Genome Res. 2004 Jun;14(6):1188-90. (PMID: 15173120)
Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700)
ACS Synth Biol. 2017 Feb 17;6(2):326-333. (PMID: 27648601)
JACS Au. 2023 Feb 27;3(3):715-735. (PMID: 37006753)
J Mol Biol. 2001 Nov 2;313(4):903-19. (PMID: 11697912)
J Cheminform. 2011 Oct 07;3:33. (PMID: 21982300)
Nat Methods. 2011 Dec 25;9(2):173-5. (PMID: 22198341)
Nat Chem. 2021 Feb;13(2):140-148. (PMID: 33380742)
Nucleic Acids Res. 2002 Apr 1;30(7):1575-84. (PMID: 11917018)
Bioinformatics. 2010 Dec 15;26(24):3075-82. (PMID: 20980272)
Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):. (PMID: 33876751)
Nat Biotechnol. 2014 Aug;32(8):834-41. (PMID: 24997786)
J Comput Chem. 2015 May 15;36(13):996-1007. (PMID: 25824339)
Chembiochem. 2019 Mar 15;20(6):800-812. (PMID: 30489013)
Angew Chem Int Ed Engl. 2021 Jan 4;60(1):88-119. (PMID: 32558088)
Nature. 2022 Apr;604(7904):86-91. (PMID: 35388195)
Science. 2015 May 22;348(6237):1261359. (PMID: 25999513)
Proc Natl Acad Sci U S A. 2018 May 8;115(19):E4358-E4367. (PMID: 29686076)
Chem Sci. 2020 May 5;11(19):5052-5057. (PMID: 34122962)
Front Genet. 2015 Jul 21;6:234. (PMID: 26257768)
Nat Biotechnol. 2021 Jan;39(1):105-114. (PMID: 32690973)
Nat Commun. 2019 Sep 13;10(1):4173. (PMID: 31519891)
معلومات مُعتمدة: ANR-21-ESRE-0021 Agence Nationale de la Recherche (French National Research Agency); ANR-19-CE07-0007 Agence Nationale de la Recherche (French National Research Agency)
المشرفين على المادة: 0 (Amines)
EC 1.5.- (Oxidoreductases Acting on CH-NH Group Donors)
تواريخ الأحداث: Date Created: 20240610 Date Completed: 20240610 Latest Revision: 20240613
رمز التحديث: 20240613
مُعرف محوري في PubMed: PMC11164908
DOI: 10.1038/s41467-024-49009-2
PMID: 38858403
قاعدة البيانات: MEDLINE
الوصف
تدمد:2041-1723
DOI:10.1038/s41467-024-49009-2