3X15

Dimeric Aquifex aeolicus cytochrome c555

Summary for 3X15

• Entry DOI: 10.2210/pdb3x15/pdb
• Related: 2ZXY
• Descriptor: Cytochrome c552, HEME C (3 entities in total)
• Functional Keywords: electron transport
• Biological source: Aquifex aeolicus VF5
• Total number of polymer chains: 4
• Total formula weight: 39533.22

Authors

Yamanaka, M.,Nagao, S.,Komori, H.,Higuchi, Y.,Hirota, S. (deposition date: 2014-10-29, release date: 2015-01-28, Last modification date: 2024-10-30)

Primary citation

Yamanaka, M.,Nagao, S.,Komori, H.,Higuchi, Y.,Hirota, S.
Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping
Protein Sci., 24:366-375, 2015

PubMed Abstract: Cytochrome c555 from hyperthermophilic bacteria Aquifex aeolicus (AA cyt c555 ) is a hyperstable protein belonging to the cyt c protein family, which possesses a unique long 310 -α-310 helix containing the heme-ligating Met61. Herein, we show that AA cyt c555 forms dimers by swapping the region containing the extra 310 -α-310 helix and C-terminal α-helix. The asymmetric unit of the crystal of dimeric AA cyt c555 contained two dimer structures, where the structure of the hinge region (Val53-Lys57) was different among all four protomers. Dimeric AA cyt c555 dissociated to monomers at 92 ± 1°C according to DSC measurements, showing that the dimer was thermostable. According to CD measurements, the secondary structures of dimeric AA cyt c555 were maintained at pH 2.2-11.0. CN(-) and CO bound to dimeric AA cyt c555 in the ferric and ferrous states, respectively, owing to the flexibility of the hinge region close to Met61 in the dimer, whereas these ligands did not bind to the monomer under the same conditions. In addition, CN(-) and CO bound to the oxidized and reduced dimer at neutral pH and a wide range of pH (pH 2.2-11.0), respectively, in a wide range of temperature (25-85°C), owing to the thermostability and pH tolerance of the dimer. These results show that the ligand binding character of hyperstable AA cyt c555 changes upon dimerization by domain swapping.

PubMed: 25586341
DOI: 10.1002/pro.2627

Experimental method

X-RAY DIFFRACTION (1.6 Å)