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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Evolutionary relationships between heme-binding ferredoxin α + β barrels

Fig. 3

Structural and sequence features of the heme-binding region in IsdG-like, OxdA, Cld/Dyp/EfeB/HemQ, and siroheme decarboxylase proteins. (a) Structure superimposition stereo diagram of the Cα backbone of IsdG-like ferredoxin-like monomer (PDB identifier 2ZDP; cyan), the C-terminal domain of OxdA-like (PDB identifier 3A16_A; red) and the C-terminal domain of Cld/DyP/EfeB/HemQ-like (PDB identifier 3NN1_A; green). (b) Stereo diagram of a ferredoxin-like domain of siroheme decarboxylase (PDB identifier 4UN1_A). In panels (a, b), heme and side chain of the heme-binding histidine is shown in stick form. c Structure-based MSA of IsdG, OxdA, Cld/Dyp/EfeB/HemQ and siroheme decarboxylase. PDB identifier/UniProt ID, organism name, start, and end for each sequence are mentioned. The region of circular permutation is indicated by ‘|’ and the sequence number around this region is colored red. The secondary structure diagram for a ferredoxin-like domain is indicated above the alignment, where arrows represent β-strands and rectangles indicate α-helices. The number of omitted residues for large insertions is boxed in green. The sequence region(s) corresponding to disorder in structure or structurally not superimposable regions is italicized. Organism abbreviations: Sa-Staphylococcus aureus, Mt-Mycobacterium tuberculosis, Bs-Bacillus subtilis, Bc-Bacillus cereus, Dr-Deinococcus radiodurans, Bt-Bacteroides thetaiotaomicron, Ap-Acetobacter pasteurianus, Aa-Alicyclobacillus acidocaldarius, Te-Taylorella equigenitalis, Cn-Candidatus nitrosoarchaeum, Al-Acholeplasma laidlawii, Bp-Beggiatoa sp., Sc-Streptococcus criceti, Er-Erysipelothrix rhusiopathiae, Ss-Staphylococcus saprophyticus, Ns-Novosphingobium sp., Kr-Ktedonobacter racemifer, Mu-Methyloversatilis universalis, At-Agrobacterium tumefaciens, Bm-Burkholderia multivorans, Sp-Streptomyces sp., Re-Rhodococcus erythropolis, Sw-Shewanella woodyi, Sl-Streptomyces albus, Am-Actinosynnema mirum, Vd-Verticillium dahliae, Vp-Variovorax paradoxus, Ko-Klebsiella oxytoca, Pm-Patulibacter medicamentivorans, Gf-Gibberella fujikuroi, Fo-Fusarium oxysporum, Pd-Penicillium digitatum, Bf-Botryotinia fuckeliana, Nf-Neosartorya fischeri, Nw-Nitrobacter winogradskyi, Tt-Thermus thermophilus, Ci-Candidatus Nitrospira, So-Shewanella oneidensis, Ba-Bjerkandera adusta, Ec-Escherichia coli, Dd-Desulfovibrio desulfuricans, Ht-Hydrogenobacter thermophilus

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