Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
03 Sep 2024
03 Sep 2024
Historique:
received:
04
05
2024
accepted:
26
08
2024
medline:
4
9
2024
pubmed:
4
9
2024
entrez:
3
9
2024
Statut:
epublish
Résumé
The inversion of substrate size specificity is an evolutionary roadblock for proteins. The Duf4243 dioxygenases GedK and BTG13 are known to catalyze the aromatic cleavage of bulky tricyclic hydroquinone. In this study, we discover a Duf4243 dioxygenase PaD that favors small monocyclic hydroquinones from the penicillic-acid biosynthetic pathway. Sequence alignments between PaD and GedK and BTG13 suggest PaD has three additional motifs, namely motifs 1-3, distributed at different positions in the protein sequence. X-ray crystal structures of PaD with the substrate at high resolution show motifs 1-3 determine three loops (loops 1-3). Most intriguing, loops 1-3 stack together at the top of the pocket, creating a lid-like tertiary structure with a narrow channel and a clearly constricted opening. This drastically changes the substrate specificity by determining the entry and binding of much smaller substrates. Further genome mining suggests Duf4243 dioxygenases with motifs 1-3 belong to an evolutionary branch that is extensively involved in the biosynthesis of natural products and has the ability to degrade diverse monocyclic hydroquinone pollutants. This study showcases how natural enzymes alter the substrate specificity fundamentally by incorporating new small motifs, with a fixed overall scaffold-architecture. It will also offer a theoretical foundation for the engineering of substrate specificity in enzymes and act as a guide for the identification of aromatic dioxygenases with distinct substrate specificities.
Identifiants
pubmed: 39227380
doi: 10.1038/s41467-024-52101-2
pii: 10.1038/s41467-024-52101-2
doi:
Substances chimiques
Dioxygenases
EC 1.13.11.-
Hydroquinones
0
Bacterial Proteins
0
hydroquinone
XV74C1N1AE
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7682Informations de copyright
© 2024. The Author(s).
Références
Jakoobi, M. & Sergeev, A. G. Transition-metal-mediated cleavage of C-C bonds in aromatic rings. Chem.-Asian J. 14, 2181–2192 (2019).
doi: 10.1002/asia.201900443
pubmed: 31051048
Qiu, X. et al. Cleaving arene rings for acyclic alkenylnitrile synthesis. Nature 597, 64–69 (2021).
doi: 10.1038/s41586-021-03801-y
pubmed: 34280952
Harayama, S., Kok, M. & Neidle, E. L. Functional and evolutionary relationships among diverse oxygenases. Annu. Rev. Microbiol. 46, 565–601 (1992).
doi: 10.1146/annurev.mi.46.100192.003025
pubmed: 1444267
Tang, H. et al. Systematic unraveling of the unsolved pathway of nicotine degradation in Pseudomonas. PLoS Genet 9, e1003923 (2013).
doi: 10.1371/journal.pgen.1003923
pubmed: 24204321
pmcid: 3812094
Fuchs, G., Boll, M. & Heider, J. Microbial degradation of aromatic compounds—from one strategy to four. Nat. Rev. Microbiol. 9, 803–816, (2011).
doi: 10.1038/nrmicro2652
pubmed: 21963803
Mariëlle J. H. et al. Hydroquinone dioxygenase from Pseudomonas Fluorescens Acb: A novel member of the family of Nonheme-Iron(Ii)-Dependent Dioxygenases. J. Bacteriol. 190, (2008).
Ronnie, J. M. et al. Discovery of novel P‑Hydroxybenzoate‑M‑Hydroxylase, Protocatechuate 3,4 Ring-Cleavage Dioxygenase, and Hydroxyquinol 1,2 Ring-Cleavage Dioxygenase from the filamentous fungus Aspergillus niger. ACS Sustain. Chem. Eng. 7, 19081–19089 (2019).
doi: 10.1021/acssuschemeng.9b04918
Semana, P. & Powlowski, J. Four aromatic intradiol ring cleavage dioxygenases from Aspergillus niger. Appl. Environ. Microbiol. 85, e01786–01719 (2019).
doi: 10.1128/AEM.01786-19
pubmed: 31540981
pmcid: 6856329
Bugg, T. D. H. & Winfield, C. J. Enzymatic cleavage of aromatic rings: mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways. Nat. Prod. Rep. 15, 513–530 (1988).
doi: 10.1039/a815513y
Tang, M. C. et al. Oxidative cyclization in natural product biosynthesis. Chem. Rev. 117, 5226–5333 (2017).
doi: 10.1021/acs.chemrev.6b00478
pubmed: 27936626
Hou, X. et al. Discovery of the biosynthetic pathway of Beticolin 1 reveals a novel non-heme iron-dependent oxygenase for anthraquinone ring cleavage. Angew. Chem. Int. Ed. 61, e202208772 (2022).
doi: 10.1002/anie.202208772
Qi, F. et al. Bienzyme-catalytic and dioxygenation-mediated anthraquinone ring opening. J. Am. Chem. Soc. 143, 16326–16331 (2021).
doi: 10.1021/jacs.1c07182
pubmed: 34586791
Vieweg, L. et al. Recent advances in the field of bioactive tetronates. Nat. Prod. Rep. 31, 1554–1584 (2014).
doi: 10.1039/C4NP00015C
pubmed: 24965099
Frisvad, J. C. A critical review of producers of small lactone Mycotoxins: Patulin, Penicillic Acid and Moniliformin. World Mycotoxin J. 11, 73–100 (2018).
doi: 10.3920/WMJ2017.2294
Alsberg, C. & Black, O. F. Contributions to the study of maize deterioration: biochemical and toxicological investigations of Penicillium Puberulum and Penicillium Stoloniferum. (US Government Printing Office, 1913).
Chan, P. K. & Hayes, A. W. The hepatobiliary toxicity of penicillic acid, a carcinogenic mycotoxin. Dev. Toxicol. Environ. Sci. 8, 507–516, (1980).
pubmed: 7308051
Nguyen, H. T. et al. Antibacterial activities of penicillic acid isolated from Aspergillus Persii against various plant pathogenic bacteria. Lett. Appl. Microbiol. 62, 488–493 (2016).
doi: 10.1111/lam.12578
pubmed: 27105128
Vieira, G. et al. Isolation and agricultural potential of penicillic acid against citrus Canker. J. Appl. Microbiol. 132, 3081–3088 (2022).
doi: 10.1111/jam.15413
pubmed: 34927315
Ciegler, A. & Kurtzman, C. P. Penicillic acid production by blue-eye fungi on various agricultural commodities. Appl. microbiol. 20, 761–764 (1970).
doi: 10.1128/am.20.5.761-764.1970
pubmed: 5485085
pmcid: 377041
Sekiguchi, J., Katayama, S. & Yamada, Y. 6-Methyl-1,2,4-Benzenetriol, a new intermediate in penicillic acid biosynthesis in Penicillium Cyclopium. Appl. l Environ. Microbiol. 53, 1531–1535 (1987).
doi: 10.1128/aem.53.7.1531-1535.1987
Seto, H., Cary, L. W. & Tanabe, M. Letter: Utilization of
doi: 10.7164/antibiotics.27.558
pubmed: 4376141
He, J. et al. Cytotoxic and other metabolites of inhabiting the rhizosphere of Sonoran desert plants. J. Nat. Prod. 67, 1985–1991 (2004).
doi: 10.1021/np040139d
pubmed: 15620238
Axberg, K. & Catenbeck, S. Intermediates in the penicillic acid biosynthesis in Penicillium Cyclopium. Acta Chem. Scand. B. 29, 749–751, (1975).
doi: 10.3891/acta.chem.scand.29b-0749
pubmed: 1189847
Axberg, K. & Gatenbeck, S. The enzymic formation of penicillic acid. FEBS Lett. 54, 18–20 (1975).
doi: 10.1016/0014-5793(75)81058-1
pubmed: 236920
Feng, P., Shang, Y., Cen, K. & Wang, C. Fungal biosynthesis of the bibenzoquinone oosporein to evade insect immunity. Proc. Natl Acad. Sci. USA 112, 11365–11370 (2015).
doi: 10.1073/pnas.1503200112
pubmed: 26305932
pmcid: 4568701
Chooi, Y. H. & Tang, Y. Navigating the fungal polyketide chemical space: from genes to molecules. J. Org. Chem. 77, 9933–9953 (2012).
doi: 10.1021/jo301592k
pubmed: 22938194
pmcid: 3500441
Bentley, R. & Keil, J. G. Tetronic acid biosynthesis in Molds. Ii. Formation of Penicillic acid in Penicillium Cyclopium. J. Biol. Chem. 237, 867–873, (1962).
doi: 10.1016/S0021-9258(18)60385-0
pubmed: 13867385
Deng, Z. et al. Mechanistic investigation on C–C bond cleavage of anthraquinone catalyzed by an atypical nonheme iron-dependent dioxygenase BTG13. ACS Catal. 797–811, (2024).
Gudgeon, J. A., Holker, J. S. & Simpson, T. J. Use of singly and doubly labelled
doi: 10.1039/c39740000636
Holker, J. S., Kaneda, M., Ramer, S. E. & Vederas, J. C. Biosynthesis of multicolosic acid, a polyketide metabolite from Penicillium Multicolor: occurrence of large
Robinson, P. K. Enzymes: Principles and biotechnological applications. Essays Biochem 59, 1–41 (2015).
doi: 10.1042/bse0590001
pubmed: 26504249
pmcid: 4692135
Arnold, F. H. Directed evolution: bringing new chemistry to life. Angew. Chem. Int. Ed. Engl. 57, 4143–4148 (2018).
doi: 10.1002/anie.201708408
pubmed: 29064156
Oue, S., Okamoto, A., Yano, T. & Kagamiyama, H. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J. Biol. Chem. 274, 2344–2349, (1999).
doi: 10.1074/jbc.274.4.2344
pubmed: 9891001
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
doi: 10.1038/nmeth.1318
pubmed: 19363495
Wang, L., Wang, Y., Wang, Q. & Liu, Y. Construction of genetic transformation system of Aspergillus Ochraceus Using Polyethylene glycol mediated method. J. Agric. Biotechnol. 24, 928–936 (2016).
Cheng, J. et al. High-level extracellular production of Α-Cyclodextrin Glycosyltransferase with recombinant Escherichia Coli BL21 (De3). J. Agric. Food Chem. 59, 3797–3802 (2011).
doi: 10.1021/jf200033m
pubmed: 21417392
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Method. Enzymol. 276, 307–326 (1997).
doi: 10.1016/S0076-6879(97)76066-X
Murshudov, G. N. et al. Refmac5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D. Biol. Crystallogr. 67, 355–367 (2011).
doi: 10.1107/S0907444911001314
pubmed: 21460454
pmcid: 3069751
Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
pubmed: 15572765