Structural Characterization of Novel Luciferase from Bioluminescence Fungi Verticillium longisporum

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A. A. Yarima
S. M. Sambo
M. D. Kwairanga
K. N. Sharbat
Z. Arifullah
A. Y. Fardami


Luciferase is an enzyme that catalyses a reaction to produce a visible light using an oxidative process, a chemical reaction that is typically referred to as bioluminescent. Insects, bacterial origin or microorganism of marine nature were considered as the mainly sources of discovered luciferase. The protein was commercialized for biomedical and biotechnological use as reporter gene. The first discovered wild form of luciferase originally from Photinu spyralis (firefly). Hence, there is need for both exploration and examination of novel luciferase to be expanded to new sources such as fungal which may likely be exploited to serve commercial purposes and applications. In this study, a novel uncharacterized luciferase protein from a fungal species Verticillium longisporum, was modelled and analysed using bioinformatic tools. The modelled 3D structure is of high quality with a PROCHECK score of 99.5%, ERRAT2 value of 91.01%, and Verify3D score of91.01%, showing that the conformational structure is acceptable. The result showed that the fungal luciferase enzyme share major characteristics with luciferase representative from various fungal and bacterial species. There is only a slight difference in the two nucleotide bindings in V. longisporum with a D/E substitution of D with E and S/T substitution. The difference of the two nucleotides binding from the two proteins may be related to the evolutionary trends. Other differences include increased number of hydrophobic and polar amino acid groups than aromatic and aliphatic ones, as well as more coils and loops with less strands. The distance between the ligand and the binding site that houses Asp 64 and Thr 110 from template proteins (Riboflavin lyaseRcaE) and Asp 543 and Thr 589 from model luciferase is similar. The only difference occurred in the V. longisporum; protein oxidoreductase activities acts on paired donors, incorporate or reduce molecular oxygen, while in the template protein oxidoreductase activities act on single donors with incorporation of molecular oxygen. This study on fungal sourced luciferase present a unique opportunity away from the more well established bacterial and insect based luciferase.

Luciferase, bioluminescent, Verticillium longisporum, protein-oxidoreductase, bioinformatic.

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How to Cite
Yarima, A. A., Sambo, S. M., Kwairanga, M. D., Sharbat, K. N., Arifullah, Z., & Fardami, A. Y. (2020). Structural Characterization of Novel Luciferase from Bioluminescence Fungi Verticillium longisporum. Biotechnology Journal International, 24(5).
Original Research Article


Kargar F, Mortazavi M, Savardashtaki A, Hosseinkhani S. Genomic and protein structure analysis of the luciferase from the Iranian bioluminescent beetle, Luciola sp. International Journal of Biological Macromolecules. 2019;124:689–698. Available:

Baldwin TO. Firefly luciferase : the structure is known , but the mystery remains. 1996;223–228.

Inouye S. Firefly luciferase: An adenylate-forming enzyme for multicatalytic functions. Cellular and Molecular Life Sciences. 2010;67(3):387–404. Available:

Vongsangnak W, Chumnanpuen P, Sriboonlert A. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ. 2016;4:2534. Available:

Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H. Structural basis for the spectral difference in luciferase bioluminescence. Nature. 2006;440(7082):372–376. Available:

Sundlov JA, Fontaine DM, Southworth, TL, Branchini BR, Gulick AM. Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism. Biochemistry. 2012;51(33):6493–6495. Available:

Smirnova DV, Ugarova NN. Invited Review Fire fly Luciferase-based Fusion Proteins and their Applications. 2017;436–447. Available:

Dragulescu-Andrasi A, Chan CT, De A, Massoud TF, Gambhir SS. Bioluminescence resonance energy transfer (BRET) imaging of protein-protein interactions within deep tissues of living subjects. Proceedings of the National Academy of Sciences, 2011;108(29):12060–12065. Available:

Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: A European ELIXIR core data resource. Nucleic Acids Research. 2019;47(D1):D542–D549. Available:

Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. The Proteomics Protocols Handbook. 2009;571–607. Available:

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology. 2011;7(539). Available:

Buchan DWA, Jones DT. The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research. 2019;47(W1):W402–W407. Available:

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. PDBsum: Structural summaries of PDB entries. Protein Science, 2018;27(1):129–134. Available:

Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Schwede T. SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research. 2018;46(W1):W296–W303. Available:

Moreno-Ulloa A, Mendez-Luna D, Beltran-Partida E, Castillo C, Guevara G, Ramirez-Sanchez I, Villarreal F. The effects of (-)-epicatechin on endothelial cells involve the G protein-coupled estrogen receptor (GPER). Pharmacological Research. 2015;100:309–320. Available:

Paxman JJ, Heras B. Bioinformatics tools and resources for analyzing protein structures. Methods in Molecular Biology. 2017;1549:209–220. Available:

Lee J. Perspectives on Bioluminescence Mechanisms. Photochemistry and Photobiology. 2017;93(2):389–404. Available:

Eljounaidi K, Lee SK, Bae H. Bacterial endophytes as potential biocontrol agents of vascular wilt diseases – Review and future prospects. Biological Control. 2016;103:62–68. Available:

Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z. UniProt Consortium on expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics (Oxford, England). 2017;33(21):3454–3460. Available:

Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Di Costanzo L, Zardecki C. RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Research. 2019;47(D1):D464–D474.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Bourne PE. The Protein Data Bank Helen. Nucleic Acids Research. 2000;28(1):235–242. Available:

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Zaretskaya I. BLAST: a more efficient report with usability improvements. Nucleic Acids Research. 2013;41(Web Server issue), 29–33. Available:

Kaskova ZM, Dörr FA, Petushkov VN, Purtov KV, Tsarkova AS, Rodionova NS, Yampolsky IV. Mechanism and color modulation of fungal bioluminescence. 2017;1–9.

Ghaemi B M, Bassami MR, Hashemi Tabar GR, Saberi MR, Haghparast AR, Dehghani H. A bioinformatic approach to check the spatial epitope structure of an immunogenic protein coded by DNA vaccine plasmids. Journal of Theoretical Biology. 2015;380:315–320. Available:

Dennis E. Desjardin AGO, Charles VS. Fungi bioluminescence revisited. Received 3rd September 2007, Accepted 3rd January 2008 First Published as an Advance Article on the Web 24th January 2008;7(2):170–182. Available: 10.1039/b713328f

Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research. 2005;33(2):244–248. Available:

Emamzadeh AR, Hosseinkhani S, Sadeghizadeh M, Nikkhah M, Chaichi MJ, Mortazavi M. cDNA Cloning, Expression and Homology Modeling of a Luciferase from the Firefly Lampyroidea maculata. BMB Reports, 2011;39(5):578–585. Available:

Panja AS, Bandopadhyay B, Maiti S. Protein thermostability is owing to their preferences to non-polar smaller volume amino acids, variations in residual physico-chemical properties and more salt-bridges. PLoS ONE. 2015;10(7):1–21. Available:

Depotter JRL, Rodriguez-Moreno L, Thomma BPHJ, Wood TA. The emerging British Verticillium longisporum population consists of aggressive Brassica pathogens. Phytopathology. 2017;107(11):1399–1405. Available:

Sheraz MA, Kazi SH, Ahmed S, Anwar Z, Ahmad I. Photo, thermal and chemical degradation of riboflavin. Beilstein Journal of Organic Chemistry. 2014;10:1999–2012. Available:

Zhou XX, Wang YB, Pan YJ, Li, WF. Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins. Amino Acids. 2008;34(1):25–33. Available:

Hui Xu, Yindrila C, Benjamin P, Angad PM, Dhananjay B, Hans-Peter H. Identification of the First Riboflavin Catabolic Gene ClusterIsolated from Microbacterium maritypicum G10. The Journal of Biological Chemistry. 2016;291(45):23506–23515.