Abstract
The soluble monomeric domain of lipoprotein YxeF from the Gram positive bacterium B. subtilis was selected by the Northeast Structural Genomics Consortium (NESG) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins. The solution NMR structure of YxeF reveals a calycin fold and distant homology with the lipocalin Blc from the Gram-negative bacterium E.coli. In particular, the characteristic β-barrel, which is open to the solvent at one end, is extremely well conserved in YxeF with respect to Blc. The identification of YxeF as the first lipocalin homologue occurring in a Gram-positive bacterium suggests that lipocalins emerged before the evolutionary divergence of Gram positive and Gram negative bacteria. Since YxeF is devoid of the α-helix that packs in all lipocalins with known structure against the β-barrel to form a second hydrophobic core, we propose to introduce a new lipocalin sub-family named ‘slim lipocalins’, with YxeF and the other members of Pfam family PF11631 to which YxeF belongs constituting the first representatives. The results presented here exemplify the impact of structural genomics to enhance our understanding of biology and to generate new biological hypotheses.
Highlights
IntroductionThe lipoprotein YxeF from Bacillus subtilis was selected by the Northeast Structural Genomics Consortium (NESG; http://www. nesg.org) as a target (gi|85674274, SwissProt/TrEMBL ID YXEF_BACSU, access number P54945, NESG target ID SR500A) of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins [1,2]
The lipoprotein YxeF from Bacillus subtilis was selected by the Northeast Structural Genomics Consortium (NESG; http://www. nesg.org) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins [1,2]
A high-quality NMR structure of the soluble domain of lipoprotein YxeF was obtained by multidimensional NMR spectroscopy [Figures 1A, 2; Table 1; PDB accession number 2JOZ]
Summary
The lipoprotein YxeF from Bacillus subtilis was selected by the Northeast Structural Genomics Consortium (NESG; http://www. nesg.org) as a target (gi|85674274, SwissProt/TrEMBL ID YXEF_BACSU, access number P54945, NESG target ID SR500A) of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins [1,2]. YxeF exhibits no significant sequence similarity with any protein with known three-dimensional structure and is one of only eight members forming Pfam [3] family PF11631 for which no functional annotation is available (Pfam 26.0 release). Bacterial lipoproteins represent a class of secreted, membraneanchored proteins that are conserved throughout bacteria and play critical roles in a wide range of biological processes, including bacterial pathogenesis and host immune response [1]. They contain a conserved N-terminal type II signal peptide known as the ‘lipobox’, which is immediately followed by an invariant Cys residue. After cleavage of the signal peptide, the lipoprotein is anchored into the bacterial membrane via a diacylglycerol moiety forming a thioether linkage to the Cys side chain as well as a fatty acid moiety coupled to the N-terminus
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