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Article

Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies

Department of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a Street, 50-383 Wrocław, Poland
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Author to whom correspondence should be addressed.
Academic Editor: Youn-Il Park
Int. J. Mol. Sci. 2021, 22(16), 8524; https://doi.org/10.3390/ijms22168524
Received: 23 June 2021 / Revised: 30 July 2021 / Accepted: 4 August 2021 / Published: 7 August 2021
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme. View Full-Text
Keywords: Rubisco; structure; photosynthesis; dinoflagelates; Symbiodinium sp.; homohexamer Rubisco; structure; photosynthesis; dinoflagelates; Symbiodinium sp.; homohexamer
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MDPI and ACS Style

Rydzy, M.; Tracz, M.; Szczepaniak, A.; Grzyb, J. Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies. Int. J. Mol. Sci. 2021, 22, 8524. https://doi.org/10.3390/ijms22168524

AMA Style

Rydzy M, Tracz M, Szczepaniak A, Grzyb J. Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies. International Journal of Molecular Sciences. 2021; 22(16):8524. https://doi.org/10.3390/ijms22168524

Chicago/Turabian Style

Rydzy, Małgorzata, Michał Tracz, Andrzej Szczepaniak, and Joanna Grzyb. 2021. "Insights into the Structure of Rubisco from Dinoflagellates-In Silico Studies" International Journal of Molecular Sciences 22, no. 16: 8524. https://doi.org/10.3390/ijms22168524

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