Structure of the Oxygen Sensor in Bacillus subtilis

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Structure of the Oxygen Sensor in Bacillus subtilis Wei Zhang, George N Phillips Structure Volume 11, Issue 9, Pages 1097-1110 (September 2003) DOI: 10.1016/S0969-2126(03)00169-2

Figure 1 The Molecular Structure of the HemAT Sensor Domain Represented with Ribbon Diagrams (A) Stereo view of the structure. The signaling domain would be located further down on the page. (B) Top view showing the flanking of the core helices, G and H, by the rest of the molecule. The helices are labeled corresponding to the nomenclature of the globin fold. Subunit A, cyan; subunit B, yellow. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 2 The Structure-Based Sequence Alignment of Sperm Whale Myoglobin (Mb_Sw), the HemAT Sensor Domain (HemAT_Bs), and Hemoglobin from Vitreoscilla stercoraria (Hb_Vs) (A) Ribbon diagrams of the three proteins in their monomeric forms and the nomenclature for the helical segments in each structure. The helical arrangement in the HemAT sensor domain is Z, A, B, C, E, F, G, and H. (B) Alignment of three amino acid sequences on the basis of their structures. Secondary structures are shown at the bottom. Identical residues between all three sequences, green; identical residues between two sequences, yellow. Similar residues are colored in cyan. The critical distal pocket Tyr and His residues and the proximal pocket His residues are shown in red letters. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 3 Error-Scaled Difference Distance Matrix (DDM) Plots of the HemAT Sensor Domain (A) DDM plot of subunit A versus subunit B within the liganded structure. (B) DDM plot of subunit A versus subunit B within the unliganded structure. The result shows that there is less dimeric symmetry in the unliganded structure. (C) DDM plot of the liganded versus unliganded structures. The changes in distances smaller than 0.7 Å are omitted. The color gradient indicates differences between 0.7 Å and 1.4 Å, where red represents expansion and blue represents contraction. The results show more-dramatic changes in subunit B, representing asymmetrical effects of the ligand departure. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 4 Ca Trace of the G and H Helices at the Dimerization Interface The unliganded structure, green; the liganded structure, yellow. These difference vectors for the G and H helices are shown in red arrows with a threshold of 0.25 Å. (A) Stereograph of side view of the helices. (B) Stereo view looking down into the cell. (C) Schematic representation of helical motions. Left, the averaged difference vectors projected onto a line parallel to the H helices. Right, the same vectors projected onto a plane perpendicular to these helices. Helices of subunit A (GA and HA), yellow; those of subunit B (GB and HB), green. The numerical values for each helix are shown with the estimated standard deviation (0.04 Å) for these helices based on error propagation of individual coordinate errors. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 5 Superposition of the Ligand Binding Sites of the Unliganded and Liganded Structures The unliganded structure, green; the liganded structure, yellow. (A) Left, side view of superposition of A sites; right, top view of A sites. (B) Left, side view of superposition of B sites; right, top view of B sites. The results show the dramatic motion of Tyr70 and the heme in the B subunit. (C) Left, electron density map of the B subunit of the liganded structure contoured at a level of 1 σ; dashed lines represent hydrogen bonds. Right, electron density map of the B subunit of the unliganded structure contoured at a level of 0.7 σ. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 6 Comparison of the Distal Pockets of the Liganded HemAT Sensor Domain and Sperm Whale Myoglobin (A) The distal pocket of the liganded HemAT sensor domain. (B) The distal pocket of the liganded sperm whale myoglobin. The result shows the deeper encapsulation of the heme in the sensor domain of HemAT. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)

Figure 7 A Model of the Four Known Types of Chemoreceptors Found in B. subtilis Type 1, purple; type 2, green; type 3, cyan; type 4, yellow. The lipid bilayer, blue and gray. The cytoplasmic domain of B. subtilis proteins is about 300 Å long, which is 40 Å longer than the cytoplasmic domain of E. coli chemoreceptors. (A) Side view of these chemoreceptors. (B) Bottom-up view from cytoplasm to periplasmic space showing how the type 4 chemoreceptors are likely to be arranged in the planar network of other receptors. Structure 2003 11, 1097-1110DOI: (10.1016/S0969-2126(03)00169-2)