The 2.6 Å resolution structure ofRhodobacter capsulatusbacterioferritin with metal-free dinuclear site and heme iron in a crystallographic `special position'

Abstract

Bacterioferritin from Rhodobacter capsulatus was crystallized and its structure was solved at 2.6 Å resolution. This first structure of a bacterioferritin from a photosynthetic organism is a spherical particle of 24 subunits displaying 432 point‐group symmetry like ferritin and bacterioferritin from Escherichia coli. Crystallized in the I422 space group, its structural analysis reveals for the first time the non‐symmetric heme molecule located on a twofold crystallographic symmetry axis. Other hemes of the protomer are situated on twofold noncrystallographic axes. Apparently, both types of sites bind heme in two orientations, leading to an average structure consisting of a symmetric 50:50 mixture, thus satisfying the crystallographic and noncrystallographic symmetry of the crystal. Five water molecules are situated close to the heme, which is bound in a hydrophobic pocket and axially coordinated by two crystallographic or noncrystallographically related methionine residues. Its ferroxidase center, in which FeII is oxidized to FeIII, is empty or fractionally occupied by a metal ion. Two positions are observed for the coordinating Glu18 side chain instead of one in the E. coli enzyme in which the site is occupied. This result suggests that the orientation of the Glu18 side chain could be constrained by this interaction.

Bis-methionyl Coordination in the Crystal Structure of the Heme-binding Domain of the Streptococcal Cell Surface Protein Shp

“…Bis-methionyl coordination has only been documented in bacterioferritin, where the thiol ether coordination comes from methionine residues on separate monomers. 28,29 Shp 180 is the first protein to show this arrangement within the same monomer. The bound heme iron is coordinated by Met66 and Met153, which are located on the α-helix and between β-strands B7 and B8, respectively ( Figure 1).…”

“…The bound heme iron is coordinated by Met66 and Met153, which are located on the α-helix and between β-strands B7 and B8, respectively ( Figure 1). The sulfur atoms are located 2.4 Å from the iron atom for both Met66 and Met153 (Figure 2(a)), comparable to the 2.1 Å -2.7 Å distance found between monomers in structures of bis-methionyl bacterioferritin [29][30][31] and to the 2.3 Å average for Fe-S distances in Fe-Cys protein structures (primarily cytochrome P450s) taken from the Protein Data Bank. 32,33 Met66 is more solvent exposed than Met153, which is in agreement with IsdC where the 3 10 -helix portion is more exposed than the β-sheet core.…”

Optical and EPR spectroscopic studies of demetallation of hemin by L-chain apoferritins

“…Since then, the presence of bacterioferritins has been established in more than 20 other prokaryotes. The X-ray structures of the bacterioferritins from Escherichia coli, R. capsulatus and, more recently D. desulfuricans have been determined [13][14][15]. The heme is localised in a hydrophobic pocket situated along the 3-fold symmetry axes, with the iron coordinated axially by two Met residues from symmetry-related subunits, and the porphyrin is clamped in place by numerous van der Waal's contacts with the protein [13].…”

2.6 Å resolution crystal structure of the bacterioferritin from Azotobacter vinelandii

“…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. Whether the heme group adopts two orientations or not perhaps depends on its interactions with surrounding residues.…”