Atomic‐resolution structure of reduced cyanobacterial cytochrome c₆ with an unusual sequence insertion

Abstract

The structure of the reduced form of cytochrome c6 from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.2 Å and refined to an R‐factor of 0.107. This protein is unique among all known cytochromes c6, owing to the presence of an unusual seven‐residue insertion, KDGSKSL(44–50), which differs from the insertion found in the recently discovered plant cytochromes c6A. Furthermore, the present protein is unusual because of its very high content (36%) of the smallest residues (glycine and alanine). The structure reveals that the overall fold of the protein is similar to that of other class I c‐type cytochromes, despite the presence of the specific insertion. The insertion is located within the most variable region of the cytochrome c6 sequence, i.e. between helices II and III. The first six residues [KDGSKS(44–49)] form a loop, whereas the last residue, Leu50, extends the N‐terminal beginning of helix III. Several specific noncovalent interactions are found inside the insertion, as well as between the insertion and the rest of the protein. The crystal structure contains three copies of the cytochrome c6 molecule per asymmetric unit, and is characterized by an unusually high packing density, with solvent occupying barely 17.58% of the crystal volume.

Crystal structures of native cytochrome c 6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization

“…A change in the space group was likewise observed for the structure of a recombinant Cyt c 6 in the PDB depositions 3dr0 (Bialek et al, 2009) Table S2). As there is no associated publication for PDB deposition 4eic, a discussion of the very small unit cell with greater than 50% sequence identity of the protein compared with PDB entry 6tr1 ( Supplementary Table S2) remains lacking.…”

“…S1 and S2). The central iron ion is hexacoordinated in a protoporphyrin derivative with histidine and methionine residues acting as axial ligands, as also revealed by the structures of cyanobacterial and green algal Cyt c 6 (Beissinger et al, 1998;Banci et al, 1998;Sawaya et al, 2001;Worrall et al, 2007;Bialek et al, 2009). Further, there is an indication that a functional class I c-type cytochrome of a chloroplast forms functionally relevant small oligomers (Kerfeld et al, 1995).…”

“…Focusing on the cyanobacteria, a high-resolution X-ray structure of recombinant cyanobacterial Cyt c 6 from Synechococcus sp. PCC 7002 (Bialek et al, 2009; PDB entry 3dr0) and the NMR structure of the native protein from Thermosynechococcus elongatus (Beissinger et al, 1998; PDB entry 1c6s) have been reported, but so far no threedimensional crystal structure of a native cyanobacterial Cyt c 6 has been described and potential oligomerization has not been addressed. Consequently, a detailed structural investigation of Cyt c 6 from its native source will help to understand the dynamic regulatory protein-protein interactions in PSI in more detail and will add another piece to a more detailed Purification and characterization of TeCyt c 6 .…”

Cytochrome c 6 of Cyanobacteria and Algae: From the Structure to the Interaction

“…Frazao et al 1995), Scenedesmus obliquus (1c6o; Schnackenberg et al 1999), Cladophora glomerata (1ls9; Dikiy et al 2002) and Chlamydomonas reinhardtii (1cyi; Kerfeld et al 1995), the red alga Porphyra yezoensis (1gdv; Yamada et al 2000) , the dun alga Hizikia fusiformis (2zbo; Akazaki et al 2008), and the cyanobacteria Synechococcus sp. (4eic; Bialek et al 2009), Synechococcus elongatus (1c6s; Beissinger et al 1998), Phormidium laminosum (2v08; Worrall et al 2007) and Arthrospira maxima (1kib; Kerfeld et al 2002). The structures of Cc 6c from Synechococcus sp.…”

“…The structures of Cc 6c from Synechococcus sp. (4eie; Bialek et al 2009) and Cc 6A from the plant Arabidopsis thaliana (2ce0; Marcaida et al 2006) A more polar heme environment stabilizes the oxidized form, thereby lowering the redox potential of the protein. This depends on structural features such as solvent accessibility of the porphyrin ring or the polarity of side chains and hydrogen bonding close to the cofactor moiety (Dikiy et al 2002).…”