The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

Abstract

The crystal structure of PA1994 from Pseudomonas aeruginosa, a member of the Pfam PF06475 family classified as a domain of unknown function (DUF1089), reveals a novel fold comprising a 15-stranded β-sheet wrapped around a single α-helix that assembles into a tight dimeric arrangement. The remote structural similarity to lipoprotein localization factors, in addition to the presence of an acidic pocket that is conserved in DUF1089 homologs, phospholipid-binding and sugar-binding proteins, indicate a role for PA1994 and the DUF1089 family in glycolipid metabolism. Genome-context analysis lends further support to the involvement of this family of proteins in glycolipid metabolism and indicates possible activation of DUF1089 homologs under conditions of bacterial cell-wall stress or host-pathogen interactions.

Figure 1

Crystal structure of PA1994 from P. aeruginosa. (a) Stereo ribbon diagram of the PA1994 monomer color coded from the N-terminus (blue) to the C-terminus (red). Helices (H1–H2) and β-strands (β1–β15) are indicated. (b) Ribbon representation of the PA1994 dimer showing domain swapping of the N-terminal β-strands. Monomers are depicted in blue and magenta. (c) Diagram showing the secondary-structure elements of PA1994 superimposed on its primary sequence. The labeling of secondary-structure elements is in accord with PDBsum (http://www.ebi.ac.uk/pdbsum), where α-helices are sequentially labeled (H1, H2, H3 etc.), β-strands are labeled (A, B, C etc.) according to the β-sheets to which they are assigned, β-turns and γ-turns are designated by Greek letters (β, γ) and β-hairpins are designated by red loops. For PA1994, the α-helix (H2), 3₁₀-helix (H1), β-strands in β-sheets (A–C), β-turns (β) and β-hairpins are indicated.

Figure 2

PA1994 exhibits structural similarity to the lipoprotein chaperones LolA and LolB. (a) Stereoview of the structural superposition of PA1994 (PDB code 2h1t, residues 2–187, blue) and LolA (PDB code 1iwl, residues 1–182, gray). (b) Stereoview of the structural superposition of PA1994 (PDB code 2h1t, residues 2–187, blue) and LolB (PDB code 1iwn, residues 10–186, gray).

Figure 3

An acidic pocket conserved in the DUF1089 family suggests a ligand-binding site. The PA1994 monomers, colored white and blue, are shown as a ribbon diagram and as a surface representation. Invariant residues (Asp101, Asp103 and Tyr147) are indicated, with the conserved Asn111 located behind the pocket labeled in parentheses. The ethylene glycol (EDO) and MPD molecules that line the entrance to the acidic pocket in the crystal are shown in green.