5B3I

Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus

Summary for 5B3I

• Entry DOI: 10.2210/pdb5b3i/pdb
• Descriptor: Cytochrome c prime, HEME C (3 entities in total)
• Functional Keywords: cytochrome c', class ii cytochrome c protein, heme protein, electron transport
• Biological source: Hydrogenophilus thermoluteolus
• Total number of polymer chains: 4
• Total formula weight: 61869.76

Authors

Fujii, S.,Oki, H.,Kawahara, K.,Yamane, D.,Yamanaka, M.,Maruno, T.,Kobayashi, Y.,Masanari, M.,Wakai, S.,Nishihara, H.,Ohkubo, T.,Sambongi, Y. (deposition date: 2016-02-29, release date: 2017-03-01, Last modification date: 2024-10-16)

Primary citation

Fujii, S.,Oki, H.,Kawahara, K.,Yamane, D.,Yamanaka, M.,Maruno, T.,Kobayashi, Y.,Masanari, M.,Wakai, S.,Nishihara, H.,Ohkubo, T.,Sambongi, Y.
Structural and functional insights into thermally stable cytochrome c' from a thermophile
Protein Sci., 26:737-748, 2017

PubMed Abstract: Thermophilic Hydrogenophilus thermoluteolus cytochrome c' (PHCP) exhibits higher thermal stability than a mesophilic counterpart, Allochromatium vinosum cytochrome c' (AVCP), which has a homo-dimeric structure and ligand-binding ability. To understand the thermal stability mechanism and ligand-binding ability of the thermally stable PHCP protein, the crystal structure of PHCP was first determined. It formed a homo-dimeric structure, the main chain root mean square deviation (rmsd) value between PHCP and AVCP being 0.65 Å. In the PHCP structure, six specific residues appeared to strengthen the heme-related and subunit-subunit interactions, which were not conserved in the AVCP structure. PHCP variants having altered subunit-subunit interactions were more severely destabilized than ones having altered heme-related interactions. The PHCP structure further revealed a ligand-binding channel and a penta-coordinated heme, as observed in the AVCP protein. A spectroscopic study clearly showed that some ligands were bound to the PHCP protein. It is concluded that the dimeric PHCP from the thermophile is effectively stabilized through heme-related and subunit-subunit interactions with conservation of the ligand-binding ability.

PubMed: 28097774
DOI: 10.1002/pro.3120

Experimental method

X-RAY DIFFRACTION (1.89 Å)