Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism

Abstract

The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.

Figure 1

Crystal structure of BB2672 from B. bronchiseptica. (a) Stereo ribbon diagram of the BB2672 protomer color-coded from the N-terminus (blue) to the C-terminus (red). Helices (H1–H6) and β-strands (β1–β7) are indicated. (b) Diagram showing the secondary-structure elements of BB2672 superimposed on its primary sequence in accordance with PDBsum (http://www.ebi.ac.uk/pdbsum). For BB2672, the α-helices (H1, H3 and H4), 3₁₀-helices (H2, H5 and H6), β-strands (β1–β7) and β-turns (β) are indicated.

Figure 2

Stereo ribbon diagrams comparing BB2672 with other related homologs. (a) Superposition of BB2672 (gray; PDB code 3byq) and SPO0826, a DUF1185 homolog from S. pomeroyi (blue; PDB code 2qtp). (b) Superposition of BB2672 (gray) with the OmpA-like domain of RmpM from N. meningitidis (blue; PDB code 1r1m) and (c) with the monofunctional chorismate mutase from B. subtilis (blue; PDB code 2cht).

Figure 3

Oligomerization states of BB2672 and monofunctional BCM. (a) Ribbon diagram of the BB2672 hexamer showing the arrangement of consecutive subunits (top view). The three molecules present in the asymmetric unit are labeled A, B and C in red. A′, B′ and C′ are the corresponding crystallographically related molecules that together form the BB2672 hexamer. Protomers with their N-terminus pointing to the front are shown in gray and those with their N-terminus pointing towards the back are shown in blue. The C-terminal ‘dimer’ interface occurs between protomers B–C, B′–C′ and A–A′. The N-terminal interface occurs between protomers A–B, A′–B′ and C–C′. (b) Ribbon diagram of the BCM trimer (PDB code 2cht, top view) showing the parallel arrangement of protomers resulting in three equivalent interfaces.

Figure 4

Stereo close-up view of the cavity in the BB2672 C-terminal ‘dimer’ interface. Conserved histidines and salt bridges are indicated.