5GYR
Tetrameric Allochromatium vinosum cytochrome c'
Summary for 5GYR
Entry DOI | 10.2210/pdb5gyr/pdb |
Related | 1bbh |
Descriptor | Cytochrome c', HEME C (3 entities in total) |
Functional Keywords | electron transport |
Biological source | Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) |
Total number of polymer chains | 8 |
Total formula weight | 115399.51 |
Authors | Yamanaka, M.,Hoshizumi, M.,Nagao, S.,Nakayama, R.,Shibata, N.,Higuchi, Y.,Hirota, S. (deposition date: 2016-09-23, release date: 2017-02-08, Last modification date: 2024-10-23) |
Primary citation | Yamanaka, M.,Hoshizumi, M.,Nagao, S.,Nakayama, R.,Shibata, N.,Higuchi, Y.,Hirota, S. Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers Protein Sci., 26:464-474, 2017 Cited by PubMed Abstract: The number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices αA and αB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein. PubMed: 27883268DOI: 10.1002/pro.3090 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
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