A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands

Abstract

Background: Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied.

Results: Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the beta-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins transcobalamin and intrinsic factor, the bacterial polysaccharide export proteins, the competence DNA receptor ComEA, the cob(I)alamin generating enzyme PduS and the Nqo1 subunit of the respiratory electron transport chain. We present evidence that members of this superfamily are likely to bind a range of soluble ligands, including B12. There are two major clades within this superfamily, namely the transcobalamin-like clade and the Nqo1-like clade. The former clade is typified by an insert of a beta-hairpin after the helix of the beta-grasp fold, whereas the latter clade is characterized by an insert between strands 4 and 5 of the core fold.

Conclusion: Members of both clades within this superfamily are predicted to interact with ligands in a similar spatial location, with their specific inserts playing a role in the process. Both clades are widely represented in bacteria suggesting that this superfamily was derived early in bacterial evolution. The animal lineage appears to have acquired the transcobalamin-like proteins from low GC Gram-positive bacteria, and this might be correlated with the emergence of the ability to utilize B12 produced by gut bacteria.

Reviewers: This article was reviewed by Andrei Osterman, Igor Zhulin, and Arcady Mushegian.

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.

Figure 2

Domain architectures and conserved gene neighborhoods of the SLBB superfamily. (A) Representative architectures are grouped according to family/clade type and labeled by gene name, organism abbreviation, and gi number; demarcated by underscores. Individual domains in architectures are depicted as colored polygons. (B) A sampling of conserved gene neighborhoods found in association with the SLBB domain, with genes depicted as boxed arrows. The SLBB members of the depicted gene neighborhoods are labeled below by gene name, organism abbreviation, and gi number; demarcated by underscores. The family/clade name of the SLBB domain is given to the left in each architecture. Names are given at the top of genes in neighborhoods, where appropriate. The large PduS operon is broken into commonly-observed gene clusters; each boxed arrow enclosed by a dotted line represents such a cluster. ComEA proteins are always in the vicinity of the two-domain ComEC protein that has an integral membrane domain predicted to form a pore through which the DNA is transported into the cell and a metallo-β-lactamase-like domain that may serve as a DNA nuclease during the uptake DNA from the outer cell wall. Additional organism abbreviations not given in Figure 1: Mhun, Methanospirillum hungatei; Mmaz, Methanosarcina mazei; Dred, Desulfotomaculum reducens; Swol, Syntrophomonas wolfei; Valg, Vibrio alginolyticus; Rleg, Rhizobium leguminosarum; and Msp, Mycobacterium sp. MCS. Additional abbreviations: SO, Sulfite Oxidoreductase; β-P, β-propeller; Fer4, 4Fe-S ferrodoxin; HTH, Helix-Turn-Helix; HhH, Helix-hairpin-Helix; RFCδ, RFC clamp loader subunit; LMW, low-molecular weight; and O-Ag, O-antigen.