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Color Plates

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COLOR PLATE 1

(Chapter 2) The structure of TatA from TatA complexes were purified in detergent solution, negatively stained with uranyl acetate, and 3D structures obtained by single-particle electron microscopy and random conical tilt reconstruction. Shown are four size classes of TatA complexes with increasing diameter. The 3D maps are filtered between 150 Å and 25 Å and contoured at 4 standard deviations above the mean density. (A) TatA complexes viewed from the closed end of the channel, proposed to be at the cytoplasmic side of the membrane (C face). Density forming the lid domain can be clearly seen. (B) TatA complexes viewed from the open end of the channel, proposed to be at the periplasmic side of the membrane (P face). (C) Side views of TatA. The front half of each molecule has been cut away to reveal internal features. (D) Views of TatA parallel to the membrane plane. The proposed position of the lipid bilayer is indicated. (Scale bar, 100 Å.) The figure was taken from Gohlke et al. (2005).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 3) Some representative crystal structures of β-barrel membrane proteins of the outer membranes of bacteria are shown. Transmembrane (TM) β-barrels have an even number of antiparallel TM strands, which is 8 for OmpA (shown here is the nuclear magnetic resonance [NMR] structure from Arora et al., 2001; for the crystal structure see Pautsch and Schulz, 1998, 2000), 10 for OmpT (Vandeputte-Rutten et al., 2001), 12 for Tsx (Ye and van den Berg, 2004), for NalP (Oomen et al., 2004), and OmPlA (Snijder et al., 1999), 14 for FadL (van den Berg et al., 2004), 16 for PhoE (Cowan et al., 1992), 18 for ScrY (Forst et al., 1998), and 22 for BtuB (Chimento et al., 2003b) and FhuA (Ferguson et al., 1998). OmpA is a small ion channel (Arora et al., 2000), OmpT is a protease, NalP is an autotransporter, FadL is a long-chain fatty acid transporter, PhoE is a diffusion pore, ScrY is a sucrose-specific porin, OmPlA is a phospholipase. BtuB and FhuA are active transporters for ferrichrome iron and vitamin B uptake, respectively. OMPs of mitochondria are predicted to form similar TM β-barrels. Examples are the VDAC channels, out of which more than a dozen have been sequenced (Heins et al., 1994). Protein structures were generated with MolMol (Koradi et al., 1996).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 3)(A) Crystal structure of the Skp trimer (PDB entry 1SG2; Korndorfer et al., 2004). The Skp trimer consists of a tightly packed 9-stranded β-barrel that is surrounded by C-terminal α-helices of the three subunits that point away from the barrel in the form of tentacles that are about 65 Å long. These tentacles form a cavity that may take up the unfolded OMP. The outside surface of the helical domain of Skp is highly basic. Each monomer of the trimeric Skp has a putative LPS binding site (Walton and Sousa, 2004) (Skp structure entry 1UM2 in the PDB). The LPS binding site was found by using a previously identified LPS binding motif (Ferguson et al., 2000) and consists of K77, R87, and R88. This motif matches the LPS binding motif in FhuA with residues K306, K351, and R382 and a root-mean-square (rms) deviation of 1.75 Å for the Cα — Cγ atoms was calculated (Walton and Sousa, 2004). Q99 in Skp may also form a hydrogen bond to an LPS phosphate, completing the four-residue LPS binding motif. (B) Crystal structure of Survival Factor A, SurA (PDB entry 1M5Y [Bitto and McKay, 2002]). The N-terminal domain (N) is composed of the α-helices H1 to H6 (residues 1 to 148) and connected to peptidyl-prolyl isomerase (PPI) domain P1 (residues 149 to 260). The P2 domain (residues 261 to 369) connects the P1 domain to the C-terminal domain C (residues 370 to 428, colored in red). Thus, the N and C domains together constitute a compact core, which is traversed by a broad deep crevice of about 50 Å in length, suggesting a polypeptide binding site. The active PPIase domain 2 (P2) is tethered to this core by two extended peptide segments. It has been demonstrated that a mutant, SurAN(-Ct), which does not contain the two PPIase domains and is composed of the N and C domains only, functions like a chaperone (Behrens et al., 2001). This SurA “core domain” has been proposed to bind the tripeptide motif aromatic-random-aromatic, which is prevalent in the aromatic girdles of α-barrel membrane proteins (Bitto and McKay, 2003). Images of the structures were created with Pymol (Delano, 2002).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 3) (A) The crystal structure of DegP (Krojer et al., 2002) is shown (PDB entry 1KY9). DegP is a homo-hexamer that is composed of two stacked rings of three DegP subunits. Drawn here is one subunit of DegP. The subunit consists of three functionally distinct domains, the protease domain (residues 1 to 259, indicated in green and in purple) and two PDZ domains, PDZ1 (residues 260 to 358, yellow) and PDZ2 (residues 359 to 448, red). The catalytic triad of the protease domain, His-105, Asp-135, and Ser-210, is located in a crevice between two β-barrel lobes with a carboxy-terminal α-helix, similar to structures of other proteases of the trypsin family. In PDZ1, the residues Arg-262, Glu-264, Leu-265, Gly-266, Ile-267, Met-268, Phe-321, Arg-325, Leu-324, and Val-328 may constitute the peptide binding site. In PDZ2, the peptide binding site may consist of residues Ser-358, Gln-359,Asn-360, Gln-361,Val-362,Asp-363, Ser-366, Gly-370, Ile-371, Glu-372, Gly-373, and Ala-374. Some of these residues of PDZ1 and PDZ2 are shown. For further details on the hexameric organization of DegP and its two different conformational states, see Krojer et al. (2002) and the supplementary information on the journal website. (B) Crystal structure of the V-shaped FkpAΔCT-dimer, i.e., an FkpA mutant, which lacks the 21 C-terminal residues (Saul et al., 2004). FkpAΔCT is shown in complex with the immunosuppressant FK506 (PDB entry 1Q6I), which binds to the FKBP-type C domain (C-Dm). Each of the 2 monomers consists of the N domain (N-Dm, residues 15 to 114), which is composed of three α-helices (formed by residues 19 to 43, 51 to 62, and 70 to 111, respectively) and functions as a chaperone. For monomer 1, this domain is shown in blue, for monomer 2 it is shown in yellow and in light green. The helices of N-Dm 1 and N-Dm 2 are tightly interlaced and maintain FkpA in dimeric form. The C domains of the two monomers are indicated in dark green (C-Dm 1) and in orange (C-Dm 2) and contain the PPIase activity. The C domains belong to the FKBP family and, in the dimer, the bound FK506 molecules are separated by about 49 Å (Saul et al., 2004). Images of the structures were created with Pymol (Delano, 2002).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 3) Folding model of OmpA. The kinetics of β-sheet secondary and β-barrel tertiary structure formation in OmpA have the same rate constants and are coupled to the insertion of OmpA into the lipid bilayer (Kleinschmidt et al., 1999a; Kleinschmidt and Tamm, 1999, 2002). The locations of the 5 tryptophans in the three identified membrane-bound folding intermediates and in the completely refolded state of OmpA (Kleinschmidt et al., 1999a; Kleinschmidt and Tamm, 1999) are shown. Additional details, such as the translocation of the long polar loops across the lipid bilayer, must still be determined. OmpA structures were generated with DeepView (Guex and Peitsch, 1997; Schwede et al., 2003).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 4) Crystal structures of LolA and LolB. The LolA and LolB molecules are each shown as a ribbon model. The structural information on LolA (1UA8) and LolB (1IWM) was obtained from the RCSB protein data bank (http://pdb.protein.osaka-u.ac.jp/pdb/) and visualized with Molscript ver 2.1.2 (http://www.avatar.se/molscript/).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 6) Model of the proteolytic cascade that degrades RseA and releases σ. (A) Noninducing conditions: σ is tightly bound to RseA in the inner membrane; DegS protease is inactive and RseP protease is inhibited by interactions with its PDZ domain and RseB and the glutamine (Q)-rich periplasmic domain of RseA, and also by DegS. (B) Initiation of the proteolytic cascade by DegS cleavage: The C termini of unassembled outer membrane porins (OMPs) bind to the PDZ domain of DegS, triggering cleavage of RseA (1), which releases the RseA periplasmic domain and bound RseB, thereby relieving negative regulation of RseP (2). (C) Release of free RseP cleavage of RseA (3) generates a membrane-free RseA with a VAA C terminus, which is an attractive substrate for cytoplasmic proteases. The released α/RseA complex is bound by ClpXP and other proteases; RseA is degraded and free σ is released (4).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 7) Disulfide bond formation in the periplasm. A protein requiring disulfide bonds for its stability is translocated into the periplasm via the SecYEG translocon with their cysteines (arbitrarily labeled C1 to C4) in a reduced state (Substrate) ➀. Disulfide bond formation is catalyzed by DsbA, either during translocation, after translocation, or a ratio of both ➁. DsbA is reoxidized back to its active oxidized state by DsbB ➂. DsbB is oxidized by ubiquinone in aerobic conditions or by menaquinone in anaerobic conditions ➂. If the substrate is misoxidized (SubstrateOxn) its disulfide bonds are isomerized to their native oxidized state (Substrate) by DsbC ➃. DsbC, DsbG, and CcmG are maintained in their active reduced state by DsbD ⡴. DsbD in turn is reduced by the cytoplasmic thioredoxin TrxA, which receives its reducing potential ultimately from cytoplasmic pools of NADPH ➅. CcmG maintains CcmH in a reduced state. Through the interaction of CcmH with CcmCDEF membrane complex, oxidized cytochrome is reduced, enabling it to form thioether covalent bonds with its heme cofactor ➆. Proteins with thioredoxin folds are in red and cysteines are in yellow. The amino acid residue numbers of the redox active cysteines are indicated.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 7) Domain organization of DsbA. Crystal structure of oxidized DsbA (PDB ID: 1FVK). The thioredoxin domain is in blue and the α-helical domain is in red. The active site disulfide bond, along with the critical proline,is indicated.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 7) The mechanism of DsbA reoxidation by DsbB. A reduced DsbA interacts with oxidized DsbB, resulting in the reoxidation of DsbA and reduction of DsbB. DsbA-DsbB complex is formed via a disulfide bond between C of DsbA and C of the second periplasmic loop of DsbB. The resolution of this complex is believed to occur through two pathways. In pathway A, a disulfide bond is formed between the first and second periplasmic loop, which is resolved by the oxidation of DsbB by quinones. In pathway B, DsbADsbB complex is resolved by quinones, without the interaction of the first periplasmic loop.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 7) Domain organization of DsbC. (A) The crystal structure of the homodimer DsbC showing the two domains (thioredoxin in blue and dimerization in green) separated by the short α-helix linker in red (PDB ID: 1EEJ). Redox active cysteines (C—C) are represented as yellow spheres and the structural disulfide bond (C—C) is indicated. (B) The molecular surface of DsbC is superimposed, visualizing the pocket formed by the dimerization of DsbC. (C) Top-down view of DsbC displaying the noncharged pocket devoid of acidic (red) and basic (blue) amino acid residues.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 12

(Chapter 7) Domain organization of DsbD. The predicted membrane topology of DsbD from the web-based program PHOBIUS (www.phobius.binf.ku.dk). The immunoglobin-like α-domain is crystallized (PDB ID: 1L6P) devoid of its signal peptide from the amino acids Arg8 to Asn. The amino acids of the β-domain from Asn to Thr are depicted as circles. The redox active cysteines (C—C) are highlighted as yellow circles. The thioredoxin-like γ-domain from Ala to Prc is crystallized (PDB ID: 1UC7). Active site cysteines in the crystal structures are shown as yellow spheres α-domain C—C and β-domain C—C). The membrane is shaded grey.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 13)

(Chapter 8 Three-dimensional structure of periplasmic folding proteins. Ribbon drawing showing the overall structure of Skp (A), PpiA (B), FkpA (C), and SurA (D), with the secondary structure elements shown in cyan α-helices) and magenta (β-strands). Structures are not shown to scale, and the Protein Data Bank identification numbers for these proteins are as follows: Skp, 1SG2; PpiA, 1J2A; FkpA, 1Q6H; SurA, 1M5Y.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 14

(Chapter 10) Proteins that mediate septum assembly in The septal ring contains at least 15 division proteins (in color). Those identified by single letters are Fts proteins. Braun’s lipoprotein and OmpA, which probably mediate constriction of the outer membrane, are shown in gray because they are not considered to be components of the septal ring. OM, outer membrane; PG, peptidoglycan; CM, cytoplasmic membrane. (Adapted with permission from the [Goehring and Beckwith, 2005].)

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 12) Schematic overview of LPS biosynthesis and assembly. The composite lipid A-core oligosaccharide (lipid A-core OS) is synthesized in the cytoplasm by the activities of the Lpx* and Waa* enzymes. It is exported across the inner membrane by the ABC transporter, MsbA. From there, lipid A core can be translocated directly to the outer membrane. Alternatively, it may provide an acceptor for environmentally regulated modifications mediated by Pag*, Pmr*, and Arn* enzymes, or for the repeat-unit O-polysaccharide (OPS). O-Polysaccharide is assembled independently by one of three known mechanisms. All begin with the transfer of a hexose-1-P or acetamidohexose-1-P to the carrier lipid, undecaprenyl phosphate, and all terminate with undecaprenyl pyrophosphate-linked polymer at the periplasmic face of the inner membrane but the transmembrane processes occurring in between are different in each pathway. The LPS molecule is completed by a ligation step mediated by the WaaL protein. The fully modified LPS molecule is then translocated by a currently unknown process to the outer membrane.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 12) Structure of lipid A and its environmentally regulated modifications in base structure of lipid A is modified by a series of enzymes that are active in the cytoplasm, the periplasm, or the outer membrane. Modifications include the nonstoichiometric addition of phosphoethanolamine or 4-aminoarabinose to the 1 and 4’ phosphates, removal of the 1-phosphate, and alterations of the acylation pattern. Many of these are regulated by the two-component regulatory systems PhoPQ (modifications in red) and PmrAB (in blue) in response to environmental signals that may reflect an intracellular lifestyle for the organism. These regulatory systems also interact. In K-12, many of these enzymes are cryptic but can be induced by growth in media containing metavanadate. In addition to enhancing resistance of the organism to host cationic antimicrobial peptides, these changes can influence LPS signaling and endotoxicity. Modifications in green are not dependent on PhoPQ or PmrAB.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 12) Schematic model of Wzy-dependent O-polysaccharide biosynthesis. (A) The formation of a hypothetical -polysaccharide composed of a tetrasaccharide -repeat unit (the four glycoses are identified by red, white, green, and blue filled circles). Undecaprenyl pyrophosphate-linked intermediates are formed at the cytoplasmic face of the membrane. These are initiated by transfer to undecaprenyl phosphate of hexose-1-P or acetamidohexose-1-P by homologs of the WbaP or WecA enzymes, respectively. The undecaprenyl pyrophosphate-linked O-repeat unit is flipped across the inner membrane by Wzx and polymerized at the periplasmic face by a blockwise process that requires Wzy and that is regulated by Wzz. (B) Modification of or -polysaccharide by lysogenic bacteriophage-encoded Gtr enzymes. The glucosyl donor is undecaprenyl phosphoryl-Glc and is synthesized by GtrB. The donor is transferred across the inner membrane by a mechanism that may involve GtrA. The serotype-specific Gtr* protein is then required for addition of glucosyl residues to the growing glycan. The reducing terminal O-repeat unit escapes modification.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 12) Schematic model of the biosynthesis of the O9a antigen by an ABC transporter-dependent pathway. The model is based on combined results from structural analysis of the LPS product and biochemical experiments. The polymer is formed by transfer of glycosyl residues to the nonreducing terminus of an undecaprenyl pyrophosphoryl-GlcNAc primer in the cytoplasm. The undecaprenyl pyrophosphatelinked intermediate (shown above) contains the identifiable primer, the adaptor domain, the repeat-unit domain, and a terminating phosphomethyl derivative whose precise linkage has not yet been resolved. The enzymes responsible for synthesis of each domain are indicated above the structure. The WbdD-mediated addition of the phosphomethyl terminator is essential for establishing modality and for recognition of the export substrate by the ABC transporter. (Modified from Raetz and Whitfield, 2002.)

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 12) Schematic model of the biosynthesis of the O:54 antigen by a synthase-dependent pathway. The polymer is formed by transfer of glycosyl residues to the nonreducing terminus of an undecaprenyl pyrophosphoryl-GlcNAc primer in the cytoplasm. The undecaprenyl pyrophosphate-linked intermediate (shown above) contains the identifiable primer, the adaptor domain, the repeat-unit domain in an overall architecture resembling the polymannans formed by ABC transporter-dependent pathways ( Color Plate 18 ). The synthase, WbbF, is required for chain extension, generating a repeat-unit domain with alternating β1,3- and β1,4-linkages. The currently available data suggest that this protein is sufficient for both chain extension and export of the nascent lipid-linked intermediate across the inner membrane. Details of the process and the mechanism by which chain termination is regulated have yet to be described. While chain extension and export are shown as separate processes, it is conceivable that they are temporally coupled in vivo. (Modified from Raetz and Whitfield, 2002.)

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 14) Organization of gene clusters in different bacteria.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 15) The biosynthesis of Moco and bis-MGD in Shown is a scheme of the biosynthetic pathway for Moco biosynthesis in and the proteins involved in these reactions. The crystal structures of MoaA from (Hanzelmann and Schindelin, 2004) and MoaC (Wuebbens et al., 2000), MoaD/MoaE (Rudolph et al., 2001), MoeA (Xiang et al., 2001), MogA (Liu et al., 2000), and MobA (Lake et al., 2000; Stevenson et al., 2000) from have been solved. In Moco is further modified by the attachment of GMP, forming MGD, and two equivalents of MGD are bound to molybdenum, forming the so-called bis-MGD cofactor. The structures were modified after the published articles.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 15) Catalytic cycle of MoaD and its interactions with MoaE and MoeB. MoaD binds in its thiocarboxylated form to MoaE, forming active MPT synthase which converts precursor Z to MPT (Rudolph et al., 2001). The MoaD-carboxylate dissociates from the complex and interacts with dimeric MoeB, and in the presence of ATP an activated MoaD-adenylate is formed (Lake et al., 2001). MoaD-AMP is susceptible to sulfuration by a protein-bound persulfide group from a sulfurtransferase. The sulfur is most likely derived from L-cysteine (Leimkuhler et al., 2001). After the formation of the thiocarboxylate group, MoaD dissociates from the MoeB dimer and reassociates with MoaE. Initial attack by the first MoaD thiocarboxylate could occur at either the C1’ or C2’ position of precursor Z to produce one of two hemisulfurated intermediates. For either intermediate structure, MPT formation would be completed by replacement of the remaining side-chain hydroxyl by the sulfhydryl from the second MoaD thiocarboxylate (Wuebbens and Rajagopalan, 2003). The structures were modified after the published articles.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 16) The ferric citrate transport and regulatory system. The signaling pathway from FecA to FecI; the involvement of TonB, ExbB, and ExbD in signaling and transport; and transport of iron through the periplasmic FecB protein and the ABC transporter FecCDE proteins are shown. Fur repressor loaded with Fe binds to the promoter upstream and and dissociates from the promoter under low-iron conditions. Interactions between the FecA TonB box and TonB and between the FecA signaling domain (residues 1 to 79 of the mature protein) and FecR (see also Color Plate 25 ) are indicated. N indicates the N-terminal end, and C is the C-terminal end of the proteins. (72 and (74 indicate FecI domains involved in binding to FecR and DNA, respectively (see also Color Plate 26 ).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 16) Predicted FecR structure derived from known crystal structures of antisigma factors. The in silico-modeling was calculated by using the Rosetta-algorithm (http://www.bioinfo.rpi.edu/~bystrc/hmmstr/about.html and presented with Swiss-PDB-ViewerV3.7 and http://www.expasy.org/spdbv. and POV-Ray V3.5). The helical regions may be approximately predicted, but their relative orientation is less certain. The N-terminal FecR structure (residues 1 to 85) is similar to the N-terminal anti-σ RseA (residues 1 to 66) crystal structure composed of four short α-helices (Campbell et al., 2003).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 25

(Chapter 16) Structure of mature FecA1—96 (Ferguson et al., 2002) deduced from NMR. The locations of suppressor mutations and single mutations that disrupt the interaction between FecA and FecR are indicated by arrows. Note that the mutations are allocated to α3, β1, and β3 (Eisenhauer et al., 2005; E. Breidenstein, S. Mahren, and V. Braun, unpublished results).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 16) Predicted FecI structure derived from known crystal structures of sigma factors. Note that all predicted sites of interaction with the —10 and —35 promoter regions, FecR, and the β’-sub-unit of the RNA polymerase are located on one side of the structure. The helical regions may be approximately predicted, but their relative orientation is less certain. The two functionally important regions 2 and 4 interconnected by region 3 are seen (see for comparison the crystal structure of σ in Campbell et al., 2003). The in silico-modeling was calculated by using the Rosetta-algorithm (http://www.bioinfo.rpi.edu/~bystrc/hmmstr/about.html and presented with Swiss-PDB-Viewer V3.7 and http://www.expasy.org/spdbv. and POV-Ray V3.5).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 27

(Chapter 17) Three-dimensional structure of the membrane-associated components BtuCD of the vitamin B (cobalamin) ABC importer. The BtuCD dimer is represented from the side of the membrane, with BtuC helices (blue and yellow, respectively) probably embedded with the lipid bilayer, which was shown between thick horizontal lines. A vanadate molecule (green) is trapped within each cytoplasmic ABC ATPase domain (green and red, respectively). The so-called EAA loop (purple) intimately interacts with the helical domain of BtuD ATPase. The model is represented by using the SwissPDB_viewer software, from atomic coordinates deposited in the Protein Data Bank (Locher et al., 2002).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 17) Three-dimensional structure of the serovar Typhimurium MsbA lipid A flippase, in complex with Mg ADP-vanadate and rough LPS. The MsbA dimer is represented from the side of the membrane, with transmembrane helices probably embedded with the lipid bilayer, which was shown between thick horizontal lines. Two LPS molecules are tightly bound to a large periplasmic loop in the protein, with the lipid A portion buried in the membrane. The ADP-vanadate molecule is trapped within a composite binding site contributed by the two cytoplasmic ABC ATPase domains. The image model is drawn by using the Swiss PDB viewer software from atomic coordinates deposited in the Protein Data Bank (Reyes and Chang, 2005).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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(Chapter 17) Three-dimensional structures of maltose-bound closed form (A) and maltose-free open form (B) of maltose-binding protein. This figure illustrates the large substrate-induced conformational change (twist and rotation) in many periplasmic substrate-binding proteins. Compare the length and the relative distance of the three arrows, which point to the same atoms in the two structures. The image model is drawn by using the SwissPDB_viewer software from atomic coordinates deposited in the Protein Data Bank (Sharff et al., 1992).

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 30

(Chapter 17) Number of ABC ATPases versus number of genes in completely sequenced genomes. The number of ABC ATPases per genome (which roughly reflects the number of ABC systems) is plotted against the total number of genes (archaea, green dots; bacteria, blue dots; eukaryotes, purple dots). Selected genomes with exceptionally high or low ABC protein content are indicated on the graph.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 31

(Chapter 18) Structure of a three-component RND-MFP-OMF efflux pump taken from the known crystal structures of AcrB (RND component [Murakami and Yamaguchi, 2003]), MexA (MFP [Akama et al., 2004a; Higgins et al., 2004]), and TolC (OMF [Koronakis et al., 2004]). (The figure was adapted from Eswaran et al. [2004] and is used with permission.)

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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COLOR PLATE 32

(Chapter 18) Structural (A) and functional (B) evidence that RND pumps export their substrates from the periplasm. (A) Side (cut-away) view of the MexB trimer (modeled on the AcrB crystal structure) with the monomer closest to the viewer removed to show the vestibule (x) between the two remaining monomers. Thus, the three vestibules in the trimer are likely portals of entry of export substrates from the periplasm into the central cavity (C), leading to the pore (P) and, finally, funnel (F) that exits the protein at the distal end of the trimer. CM, cytoplasmic membrane; PP, periplasm. (Adapted from Poole [2004c] and used with permission.) (B) Model of Cu efflux by the CusCBA RND-type efflux system, highlighting its export of Cu from the periplasm. CusF is a periplasmic Cu-binding protein that works with CusCBA to export Cu from the cell, consistent with CusCBA being able to accommodate periplasmic Cu. CopA is a CM ATPase that exports cytoplasmic Cu, and mutants lacking this pump show a Cu-sensitive phenotype that is not compensated for by CusCBA, arguing that CusCBA is not an alternative pump for removal of cytoplasmic Cu. Thus, Cu entering the periplasm from the extracellular milieu or from the cytoplasm (via CopA) is exported via CusCBA with or without CusF involvement.

Citation: Ehrmann M. 2007. Color Plates, In The Periplasm. ASM Press, Washington, DC.
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