Structure prediction for the di-heme cytochrome b 561 protein family

Abstract

Atomic models possessing the common structural features identified for the cytochrome b(561) (cyt b(561)) protein family are presented. A detailed and extensive sequence analysis was performed in order to identify and characterize protein sequences in this family of transmembrane electron transport proteins. According to transmembrane helix predictions, all sequences contain 6 transmembrane helices of which 2-6 are located closely in the same regions of the 26 sequences in the alignment. A mammalian ( Homo sapiens) and a plant ( Arabidopsis thaliana) sequence were selected to build 3-dimensional structures at atomic detail using molecular modeling tools. The main structural constraints included the 2 pairs of heme-ligating His residues that are fully conserved in the family and the lipid-facing sides of the helices, which were also very well conserved. The current paper proposes 3-dimensional structures which to our knowledge are the first ones for any protein in the cyt b(561) family. The highly conserved His residues anchoring the two hemes on the cytoplasmic side and noncytoplasmic side of the membrane are in all proteins located in the transmembrane helices 2, 4 and 3, 5, respectively. Several highly conserved amino acids with aromatic side chain are identified between the two heme ligation sites. These residues may constitute a putative transmembrane electron transport pathway. The present study demonstrates that the structural features in the cyt b(561) family are well conserved at both the sequence and the protein level. The central 4-helix core represents a transmembrane electron transfer architecture that is highly conserved in eukaryotic species.

Axial Ligation and Stoichiometry of Heme Centers in Adrenal Cytochromeb561

“…Earlier topological analyses (3,35,49) have convincingly positioned the His54/His122 pair near the matrix (M) surface of the CG membrane and the His88/His161 pair near the membrane's cytoplasmic (C) surface (Fig. 9).…”

“…7). Third, in the framework of the model of Bashtovyy et al (3) it is conceivable that when His88 is mutated it can be replaced by His 92. However, the model does not have any histidine residues that could replace His54, His122 and His161 as axial ligands.…”

Tumor Suppressor 101F6 and Ascorbate Synergistically and Selectively Inhibit Non–Small Cell Lung Cancer Growth by Caspase-Independent Apoptosis and Autophagy

“…A computer-aided homologous structure analysis of the 101F6 protein predicted it to be a member of the di-heme cytochrome b561 (Cyt b 561 ) protein family, as shown by a more than 90% alignment of its consensus amino acid sequence within the transmembrane domain of the Cyt b 561 (5,6). The Cyt b 561 family of proteins constitutes a class of intrinsic high-redox-potential membrane proteins containing two heme molecules that are involved in the regeneration and homeostasis of ascorbate (ascorbic acid, vitamin C) and has been shown to play an important role in a wide variety of physiologic processes, including iron uptake, cell defense, nitrate reduction, and signal transduction (5)(6)(7)(8).…”

“…The Cyt b 561 family of proteins constitutes a class of intrinsic high-redox-potential membrane proteins containing two heme molecules that are involved in the regeneration and homeostasis of ascorbate (ascorbic acid, vitamin C) and has been shown to play an important role in a wide variety of physiologic processes, including iron uptake, cell defense, nitrate reduction, and signal transduction (5)(6)(7)(8). Cyt b 561 has been identified in a large number of phylogenetically distant species, and most species contain three or four Cyt b 561 paralogous proteins.…”

Auxin-Responsive Genes AIR12 Code for a New Family of Plasma Membrane b-Type Cytochromes Specific to Flowering Plants

“…One heme is predicted to be close to an ascorbate binding site facing the cytosol, whereas the second heme faces the opposite side of the membrane and can be oxidized by either MDA or ferrichelates (Tsubaki et al, 1997;McKie et al, 2001;Bérczi et al, 2005;Kamensky et al, 2007). Plants contain several orthologous genes to animal cytochrome b561 Bashtovyy et al, 2003). Arabidopsis (Arabidopsis thaliana) contains four genes belonging to this family (Tsubaki et al, 2005) and one of these (At4g25570, CYBASC1), expressed in recombinant form, showed similar biochemical properties to animal cytochrome b561 (Bérczi et al, 2007).…”