3VYM

Dimeric Hydrogenobacter thermophilus cytochrome c552

Summary for 3VYM

• Entry DOI: 10.2210/pdb3vym/pdb
• Descriptor: Cytochrome c-552, HEME C (3 entities in total)
• Functional Keywords: electron transport
• Biological source: Hydrogenobacter thermophilus
• Total number of polymer chains: 1
• Total formula weight: 9204.52

Authors

Hayashi, Y.,Nagao, S.,Osuka, H.,Komori, H.,Higuchi, Y.,Hirota, S. (deposition date: 2012-09-28, release date: 2012-11-07, Last modification date: 2024-10-09)

Primary citation

Hayashi, Y.,Nagao, S.,Osuka, H.,Komori, H.,Higuchi, Y.,Hirota, S.
Domain Swapping of the Heme and N-Terminal alpha-Helix in Hydrogenobacter thermophilus Cytochrome c(552) Dimer
Biochemistry, 51:8608-8616, 2012

PubMed Abstract: Oxidized horse cytochrome c (cyt c) has been shown to oligomerize by domain swapping its C-terminal helix successively. We show that the structural and thermodynamic properties of dimeric Hydrogenobacter thermophilus (HT) cytochrome c(552) (cyt c(552)) and dimeric horse cyt c are different, although both proteins belong to the cyt c superfamily. Optical absorption and circular dichroism spectra of oxidized dimeric HT cyt c(552) were identical to the corresponding spectra of its monomer. Dimeric HT cyt c(552) exhibited a domain-swapped structure, where the N-terminal α-helix together with the heme was exchanged between protomers. Since a relatively strong H-bond network was formed at the loop around the heme-coordinating Met, the C-terminal α-helix did not dissociate from the rest of the protein in dimeric HT cyt c(552). The packing of the amino acid residues important for thermostability in monomeric HT cyt c(552) were maintained in its dimer, and thus, dimeric HT cyt c(552) exhibited high thermostability. Although the midpoint redox potential shifted from 240 ± 2 to 213 ± 2 mV by dimerization, it was maintained relatively high. Ethanol has been shown to decrease both the activation enthalpy and activation entropy for the dissociation of the dimer to monomers from 140 ± 9 to 110 ± 5 kcal/mol and 310 ± 30 to 270 ± 20 cal/(mol·K), respectively. Enthalpy change for the dissociation of the dimer to monomers was positive (14 ± 2 kcal/mol per protomer unit). These results give new insights into factors governing the swapping region and thermodynamic properties of domain swapping.

PubMed: 23035813
DOI: 10.1021/bi3011303

Experimental method

X-RAY DIFFRACTION (2 Å)