9L08

Cyclic Trimer of Helix-Linked Cytochrome c555

Summary for 9L08

• Entry DOI: 10.2210/pdb9l08/pdb
• Descriptor: Covalently Connected Cytochrome c555 trimer, HEME C, SULFATE ION, ... (7 entities in total)
• Functional Keywords: cyclic protein, cytochrome c, electron transfer, heme protein, sortase a-mediated ligation, nanoporous structure, electron transport
• Biological source: Aquifex aeolicus VF5
• Total number of polymer chains: 2
• Total formula weight: 67005.98

Authors

Novientri, G.,Mashima, T.,Matsuura, H.,Ogata, H.,Hirota, S. (deposition date: 2024-12-12, release date: 2025-05-28)

Primary citation

Novientri, G.,Fujiwara, K.,Mashima, T.,Matsuura, H.,Ogata, H.,Uchihashi, T.,Fujii, S.,Sambongi, Y.,Hirota, S.
Construction of a Cyclic Regular-Triangle Trimer of Cytochrome c 555 with a Central Hole Using Sortase A.
Chemistry, 31:e202404736-e202404736, 2025

PubMed Abstract: Protein-based supramolecules require precise arrangement of building blocks. A regular-triangle trimer (cp-c) has been constructed using an α-helix-inserted-circular permutant (cp-c) of Aquifex aeolicus cytochrome (cyt) c, where the trimers may dissociate to monomers. In this study, we stabilized the regular-triangle structure by constructing a cyclic regular-triangle of three α-helix-linked cyt c molecules using sortase-mediated ligation (SML). Comparing SML using sortase A for six cp-c variant trimers, the variant with GGG at the N-terminus and LPETG at the C-terminus reacted most efficiently. OP-(c) was designed, in which two cyt c molecules were fused using an α-helix, generating a dimer. The cyt c C-terminal region was attached to the N-terminus of the dimer, and the cyt c N-terminal region was attached to the C-terminus of the dimer using the same α-helix. OP-(c) was expressed in Escherichia coli cells, and the termini were connected by SML, forming a cyclic regular-triangle, CL-(c). CL-(c) showed higher thermostability than (cp-c) and OP-(c). CL-(c) structural stability was confirmed using high-speed atomic force microscopy. The X-ray crystal structure of CL-(c) showed a cyclic structure and a nanoporous supramolecular assembly. These results demonstrate that a nanoporous supramolecular assembly can be constructed by designing a cyclic molecule with a central hole using SML.

PubMed: 40148242
DOI: 10.1002/chem.202404736

Experimental method

X-RAY DIFFRACTION (1.6 Å)