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Figure 1 | Biology Direct

Figure 1

From: A novel superfamily containing the β-grasp fold involved in binding diverse soluble ligands

Figure 1

Topology diagram of SLBB domain and multiple alignment of the SLBB superfamily. (A) The five-stranded core (characteristic of all members of the βG-F) is shown with the helical face at the near side. β-strands are depicted as blue arrows, with the arrowhead at the C-terminus while the α-helix is shown in red. The two-strand insertion in the Transcobalamin-like clade is colored in yellow and enclosed in a dotted box. The insertion point for the Nqo1-like clade is marked by a red box. The approximate soluble ligand-binding spatial region is marked by a green oval. Residues known to contribute to cobalamin binding as derived from the crystal structure of Transcobalamin are shown as small circles. Orange circles indicate sidechain-mediated interactions while greenish blue circles indicate backbone or backbone and sidechain-mediated interactions. The conservation of an aromatic residue in Transcobalamin proteins is represented by a phenylalanine residue, rendered as a line drawing and colored purple. (B) Proteins are denoted by their gene names, species abbreviations, and gi numbers; demarcated by underscores. Amino acid residues are colored according to sidechain properties and degree of conservation within the alignment, set at 80% consensus. Consensus abbreviations are shown below the alignment. The secondary structure shown above the alignment is derived from the crystal structures of Transcobalamin and Nqo1 and secondary structure prediction programs. E and H denote β-strand and α-helix, respectively. Secondary structure elements conserved across the SLBB superfamily are labeled in the top line of the alignment. "Insert #1" refers to the Transcobalamin-like clade insert while "Insert #2" refers to the Nqo1-like clade insert. "asc" refers to the ascending connector between strands 4 and 5 often observed in the β-grasp fold. The consensus abbreviations and coloring scheme are as follows: h, hydrophobic residues (ACFILMVWY) shaded yellow; s, small residues (AGSVCDN) colored blue; p, polar residues (STEDKRNQHC) colored purple; and b, big residues (LIYERFQKMW) shaded gray. The conserved glycine residues characteristic of this superfamily are shaded light green and colored white. Species abbreviations are as follows: Aae: Aquifex aeolicus; Amel: Apis mellifera; Ana: Nostoc sp.; Bcer: Bacillus cereus; Bmar: Blastopirellula marina; Bthu: Bacillus thuringiensis; Cglu: Corynebacterium glutamicum; Ctet: Clostridium tetani; Dhaf: Desulfitobacterium hafniense; Dmel: Drosophila melanogaster; Ecol: Escherichia coli; Hinf: Haemophilus influenzae; Hsap: Homo sapiens; Krad: Kineococcus radiotolerans; Lint: Leptospira interrogans; Lmon: Listeria monocytogenes; Lreu: Lactobacillus reuteri; Lsak: Lactobacillus sakei; Mace: Methanosarcina acetivorans; Mbur: Methanococcoides burtonii; Moth: Moorella thermoacetica; Nham: Nitrobacter hamburgensis; Oihe: Oceanobacillus iheyensis; Ppro: Photobacterium profundum; Psyr: Pseudomonas syringae; Rbal: Rhodopirellula baltica; Sent: Salmonella enterica; Sepi: Staphylococcus epidermidis; Sfum: Syntrophobacter fumaroxidans; Spyo: Streptococcus pyogenes; Sthe: Streptococcus thermophilus; Styp: Salmonella typhimurium; Susi: Solibacter usitatus; Syn: Synechococcus sp.; Tmar: Thermotoga maritima; Tnig: Tetraodon nigroviridis; and Tthe: Thermus thermophilus.

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