Pathway of polyisoprenoid chain biosynthesis. In E. coli, the major quinones are ubiquinone-8 (UQ-8), menaquinone-8 (MK-8), and demethylmenaquinone-8 (DMK-8), where -8 refers to eight isoprenoid units in the side chain (Collins and Jones 1981). In T. thermophilus, MK-8 is the major quinone (Collins and Jones 1981).

Overall structure of TT1927b with the bound ligand (stereo view). The α-helix is red, the β-strands are cyan, the 3₁₀ helix is green, and the random coils are gray. An octaprenylpyrophosphate molecule is bound in the hydrophobic pore of the eight-stranded barrel. The isoprenoid chain, phosphorus atoms, and oxygen atoms of the ligand are colored yellow, orange, and red, respectively. The figure was drawn using MOLSCRIPT (Kraulis 1991) and RASTER3D (Merritt and Bacon 1997).

Difference electron density for the octaprenylpyrophosphate (stereo view). A simulated annealing omit α_calc(|_o| − |F_c|) map was calculated without the ligand atoms to 1.65 Å resolution and contoured at 3.0 σ. The figure is in the same orientation as in Figure 3 ▶. The carbon, phosphorus, and oxygen atoms of the octaprenylpyrophosphate are represented in yellow, orange, and red, respectively. The carbon, oxygen, and nitrogen atoms of the protein are represented in green, red, and blue, respectively. Hydrogen bonds between the phosphate group in octaprenylpyrophosphate and Arg62 are represented by red dotted lines.

Cα superposition of TT1927b with its structural homologs (stereo view). The figure is in the same orientation as in Figure 3 ▶. TT1927b and its structural homologs are displayed in blue and red, respectively. (A) Superposition of TT1927b with the OmpA transmembrane domain. The OmpA model (PDB code 1bxw-A) consists of residues 1–171. The disordered regions are represented by dotted lines. (B) Superposition of TT1927b with αd2 of QHNDH. The QHNDH model (PDB code 1jju-A) consists of residues 174–273. (C) Superposition of TT1927b with RBP. The RBP model (PDB code 1aqb) consists of residues 21–140.

Sequence comparison between TT1927b and its thirteen closest homologs. The figure was constructed by PSI-BLAST (Altschul et al. 1997) followed by CLUSTALW (Thompson et al. 1994). The first column shows the protein identifier. All proteins are annotated as hypothetical or uncharacterized proteins: Ca, Chloroflexus aurantiacus; Sa, Streptomyces avermitilis; Lm, Listeria monocytogenes; Gm, Geobacter metallireducens; Li, Listeria innocua; Sc, Streptomyces coelicolor; Ce, Corynebacterium efficiens; Se, Salmonella enterica; Tf, Thermobifida fusca; YceI_Ec, YceI from E. coli. “I”, “H”, and “E” represent percent identity, percent homology, and E-values from the PSI-BLAST results, respectively. Strictly conserved and similar residues are represented within a red box and in red letters, respectively. Residues that recognize the isoprenoid chain of the ligand with their main chains and side chains are indicated by open green squares and circles, respectively. Residues that contact the phosphate group of the ligand with their side chains are indicated by open red circles. Arg62, with a side chain that contacts and forms a hydrogen bond with the phosphate group of the ligand, is indicated by a filled red circle.

Topology diagram of TT1927b, as viewed from the outside of the barrel. Residues in β-strands are shown in squares, those in coils are shown in circles, those in α-helices are shown in pentagons, and those in the 3₁₀-helix are shown in diamonds. Residues that recognize the isoprenoid chain of the ligand with their side chains are highlighted in green. Arg17, with a main-chain carbonyl group that forms a VDW contact with the isoprenoid chain, is represented within a green box. His18, Arg62, His65, and Trp146, with side chains that form hydrophobic or VDW contacts with the phosphate group of the ligand, are highlighted by red frames. Arg62, with an Nh atom that forms a hydrogen bond with the phosphate group of the ligand, is represented by a red letter.

Crystallographic B-factors of TT1927b. The protein chain is colored according to the B-factor values, with lower values in blue and higher values in red.