24NK

Crystal Structure of Cypridina Luciferase complexed with Oxyluciferin

This is a non-PDB format compatible entry.

Summary for 24NK

• Entry DOI: 10.2210/pdb24nk/pdb
• Related: 24NE
• Descriptor: Luciferase, 2-acetamido-2-deoxy-beta-D-glucopyranose, (2~{S})-~{N}-[3-[3-[bis(azanyl)methylideneamino]propyl]-5-(1~{H}-indol-3-yl)pyrazin-2-yl]-2-methyl-butanamide (3 entities in total)
• Functional Keywords: luciferase, luminescent protein
• Biological source: Cypridina noctiluca
• Total number of polymer chains: 1
• Total formula weight: 60598.13

Authors

Kihira, K.,Wu, C.,Kanie, S.,Yasuno, R.,Mitani, Y.,Ohmiya, Y. (deposition date: 2026-03-12, release date: 2026-04-08)

Primary citation

Kihira, K.,Yasuno, R.,Kanie, S.,Wu, C.,Mitani, Y.,Ohmiya, Y.
Three-dimensional structure of Cypridina luciferase illuminates the mechanism of bioluminescence of imidazopyrazinone-type luciferin.
Int.J.Biol.Macromol., 357:151583-151583, 2026

PubMed Abstract: Bioluminescence occurs in marine organisms and involves the oxidation of imidazopyrazinone-type luciferin catalyzed by luciferase. Although chemiluminescence mechanisms have been studied using luciferin analogs in aprotic solvents, the enzymatic reaction within luciferase remains poorly understood due to the lack of structural information. Cypridina luciferin (CypL), used by Vargula hilgendorfii, is an imidazopyrazinone compound known for its high quantum yield and turnover rate. Here, we report the crystal structure of Cypridina luciferase (CLuc) and its reaction product, Cypridina oxyluciferin (CypOL). Structural analysis and mutagenesis suggest that the amino acid residue H542 may mediate either deprotonation at the N7 position or stabilization of the anionic form of CypL in the first step of the oxidation process. This mechanism, together with strict substrate recognition, would provide a clue to investigate the molecular basis of CLuc's efficient light emission and advance understanding of imidazopyrazinone-type bioluminescence.

PubMed: 41865923
DOI: 10.1016/j.ijbiomac.2026.151583

Experimental method

X-RAY DIFFRACTION (3.14 Å)