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5GYR

Tetrameric Allochromatium vinosum cytochrome c'

Summary for 5GYR
Entry DOI10.2210/pdb5gyr/pdb
Related1bbh
DescriptorCytochrome c', HEME C (3 entities in total)
Functional Keywordselectron transport
Biological sourceAllochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
Total number of polymer chains8
Total formula weight115399.51
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 citationYamanaka, 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: 27883268
DOI: 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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数据于2025-07-02公开中

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