Journal: PLoS ONE
Article Title: NMR Structure of Lipoprotein YxeF from Bacillus subtilis Reveals a Calycin Fold and Distant Homology with the Lipocalin Blc from Escherichia coli
doi: 10.1371/journal.pone.0037404
Figure Lengend Snippet: Surface electrostatic potential calculated for (A) the YxeF NMR structure (first conformer of ensemble deposited in the PDB) and (B) the homology model of A7ZAF5 by using the program GRASP accessed through the protein function annotation server MarkUs . The homology model was calculated using the SWISS-MODEL server in alignment mode , and Verify3D , Procheck and ProsaII all atom z-scores (-1.12, −3.43 and −1.61, respectively) were obtained using the PSVS server and are indicative of a good quality model. In (C) and (D), ribbon drawings are shown for the structures of YxeF and A7ZAF5 in the same orientation, that is, viewed on the open end of the β-barrels. The acidic residues giving rise to the negative potential inside the cavities are depicted in licorice representation and are labeled (black for YxeF, red for A7ZAF5). (E) Pfam multiple alignment of the sequences of all members of PF11631. Except for YxeF (P54945), the sequences are labeled with their UniProt IDs (D4G3V0, E8VFY0, E0TYE6, D5MWC1, E3E109, A7ZAF5, E1UTS8). Amino acid background colors reflect average similarity inferred from the Blosum62 matrix, ranging from ‘most conserved’ (black) to ‘least conserved’ (white). YxeF and A7ZAF5 are highlighted in bold on the left and the region of the alignment used for building the comparative model of A7ZAF5 from the YxeF structure is enclosed by red boxes. The acidic residues labeled in (C) and (D) are marked with black (YxeF) and red (A7ZAF5) asterisks, respectively, above or below the alignment.
Article Snippet: The only proteins known to share significant sequence identity with YxeF are found in the Bacillus genus, e.g. , D5MWC1 from B. subtilis strain ATCC 6633, E3E109 form B. atrophaeus strain 1942, and the somewhat more distant homolog A7ZAF5 from B. amyloliquefaciens (61% identity; member of PF11631; see for a multiple sequence alignment of all members).
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