Structure of a Monoclinic Crystal Form of Cytochrome b1 (Bacterioferritin) from E. coli

Abstract

Crystals of E. coli cytochrome b l, alias bacterioferritin, were grown from a low ionic strength solution. The resulting monoclinic P21 structure was solved by molecular replacement and refined using noncrystallographic symmetries applied to the fundamental unit, consisting of two protein subunits and a single haem. From the Patterson self-rotation results it was shown that the asymmetric unit of the monoclinic crystal consists of 12 such dimers and corresponds to a complete, nearly spherical, molecule of bacterioferritin (Mr = 450 kDa) of 432 point-group symmetry. It is thus the most symmetrical cytochrome. As previously determined for the tetragonal form, the haem is located in a special position on a local twofold axis of the dimer. A bimetal centre is also observed within the four-helix bundle of each monomer; a metal-binding site is located on the fourfold axis. discovery in

2.6 Å resolution crystal structure of the bacterioferritin from Azotobacter vinelandii

“…The reasonable averaged B factor 24.67 A 2 of Ba 2þ is close to that of its coordinated oxygen atoms, 22.24 A 2 . As in the case of EcBF [17], the fourfold channel in AvBF is extremely hydrophilic with an upper layer of four Asnl48 residues on the external surface of the protein shell and a lower layer of four Gln151 residues on the inner face (Fig. 4).…”

“…The top layer defines the entrance and includes Asn17, Ile20, Leu93 and Gly97; the middle layer defines the side walls and mainly includes residues Ala21, Try25 and Leu101; and the bottom layer is mainly composed of Glu47, Asp50, His54, Asp129, His130 and Ser126. Structural comparison reveals that the dinuclear iron center of AvBF has two significant structural features different from those of EcBF [17] and DdBF [11]. First, the Fe1 atom in AvBF has both a low occupancy (0.54 on average) and a long distance to Fe2.…”

“…The search template was the octamer composed of the monomers A, B, C, D, K, L, U and V from the crystal structure of Escherichia coli bacterioferritin (EcBF) with PDB accession code 1BFR [17]. On the first run of EPMR, the best solution was found with a crystallographic R factor of 0.362 and a correlation coefficient 0.675.…”

“…This means that the heme cofactor is located in a right position and orientation, but is not disordered or in a mixture of two orientations. Therefore, we consider that the heme preferentially binds to AvBF protein in one orientation, similar to the case of EcBF [17,21]. However, in the structures of both Rhodobacter capsulatus bacterioferritin (RcBF) [22] and DdBF [11], the heme groups were defined with two possible orientations each with an occupancy of about 0.50.…”

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“…3b). [85][86][87] Each of the four-helix-bundle subunits of BFR contains a dinuclear metal binding site. The site binds two Fe II atoms with histidine (H54 and H130) and glutamate (E51, E18, E127 and E94) residues as capping ligands.…”