Bacterial barrel structure

In green plants, which contain little or no cholesterol, cydoartenol is the key intermediate in sterol biosynthesis.161-1623 As indicated in Fig. 22-6, step c, cydoartenol can be formed if the proton at C-9 is shifted (as a hydride ion) to displace the methyl group from C-8. A proton is lost from the adjacent methyl group to close the cyclopropane ring. There are still other ways in which squalene is cyclized,162/163/1633 including some that incorporate nitrogen atoms and form alkaloids.1631 One pathway leads to the hop-anoids. These triterpene derivatives function in bacterial membranes, probably much as cholesterol does in our membranes. The three-dimensional structure of a bacterial hopene synthase is known.164 1643 Like glucoamylase (Fig. 2-29) and farnesyl transferase, the enzyme has an (a,a)6-barrel structure in one domain and a somewhat similar barrel in a second domain. 

VDAC plays a role in the regulated flux of metabolites—usually anionic species such as phosphate, chloride, organic anions, and the adenine nucleotides—across the outer membrane. VDAC appears to form an open p -barrel structure similar to that of the bacterial porins (Section 12.5.2). although mitochondrial porins and bacterial porins may have evolved independently. Some cytoplasmic kinases bind to VDAC, thereby obtaining preferential access to the exported ATP. In contrast, the inner membrane is intrinsically impermeable to nearly all ions and polar molecules. A large family of transporters shuttles metabolites such as ATP, pyruvate, and citrate across the inner mitochondrial membrane. The two faces of this membrane will be referred to as the matrix side and the cytosolic side (the latter because it is freely accessible to most small molecules in the cytosol). They are also called the N and P sides, respectively, because the membrane potential is negative on the matrix side and positive on the cytosolic side. 

This a-domain is common to all class I terpene synthases and is the only domain in bacterial and fungal class I enzymes such as the pentalenene synthase from Streptomyces ey oliatus or the trichodiene synthase from Fusarium sporotri-chioides (Fig. 87.14a) [191,194]. Plant hemi-, mono-, and sesquiterpene synthases exhibit a second helical p-domain that resembles a barrel structure. An example of this class is given by the (+)-5-cadinene synthase from G. arboreum (Fig. 87.14b) [195]. In plant diterpene cyclases and in the exceptional case of the ( )-a-bisabolene synthase from A. grandis (Fig. 87.14c), a third helical y-domain with a barrel-like structure is present [197, 200, 202]. The p- and y-domains in the plant enzymes are nonfunctional but are required for correct enzyme folding. 

Sparks, J.M. and Baldwin, T.O., Functional imphcations of the unstructured loop in the (P/a)g barrel structure of the bacterial ludferase a subunit, Biochemistry, 40, 15436, 2001. 

Typically, functional porins are homotrimers, which assemble from monomers and then integrate into the outer membrane. The general porins, water-filled diffusion pores, allow the passage of hydrophilic molecules up to a size of approximately 600 Daltons. They do not show particular substrate specificity, but display some selectivity for either anions or cations, and some discrimination with respect to the size of the solutes. The first published crystal structure of a bacterial porin was that of R. capsulatus [48]. Together with the atomic structures of two proteins from E. coli, the phosphate limitation-induced anion-selective PhoE porin and the osmotically regulated cation-selective OmpF porin, a common scheme was found [49]. Each monomer consists of 16 (3-strands spanning the outer membrane and forming a barrel-like structure. 

Buchanan, S. K. (1999). Beta-barrel proteins from bacterial outer membranes structure, function and refolding, Curr. Opin. Struct. Biol., 9, 455-461. 

Striking is the resemblance between our model structure and the multi-stranded -barrels known for various membrane proteins [42] and poreforming toxins [43]. The formation of an aqueous pore in the lipid bilayer would indeed offer an explanation for the observed bilayer conductivity induced by gramicidin S upon membrane binding [6]. The peptidedipid ratio of 1 40 at which this structure could be trapped for NMR analysis appears to be biologically relevant, as the minimum inhibitory concentration of gramicidin S corresponds to far more than an equimolar ratio of peptides per lipid molecule on the bacterial surface [34,35]. 

Bishop, R.E. Structural biology of membrane-intrinsic beta-barrel enzymes sentinels of the bacterial outer membrane. Biochim Biophys Acta 1778 (2008) 1881-1896. 

Crystal structures exist of two bacterial PI-PLC enzymes, the protein from B. cereus (Heinz et al., 1995), which can cleave GPI-anchors, and the PI-PLC from Listeria monocytogenes (Moser et al., 1997), which is not able to effectively release GPI-anchored proteins. While the sequence homology of these two proteins is limited, the structures are very similar. The bacterial PI-PLC proteins are folded into a distorted TIM-barrel, where the parallel (3-strands form an inner circular and closed barrel with a-helices located on the outside between neighboring (3-strands, that is structurally very similar to the catalytic domain of PLC8j, the only mammalian PI-PLC for which there is a structure (Essen et al., 1996 Heinz et al., 1998). The availability of structures and results of mutagenesis provide details on the catalytic mechanism for this type of enzyme (for review and more extensive references see Mihai et al. (2003)). 

In the bacterial PI-PLC structures, the top of the barrel rim has several hydrophobic residues that are fully exposed to solvent and poorly defined in the crystal structures (implying significant mobility). The active site of PI-PLC is accessible and well-hydrated, and these mobile elements at the top of the barrel offer a different motif for interactions of the protein with phospholipid interfaces. The PI-PLC from B. thuringiensis (nearly identical in sequence to the enzyme from B. cereus whose crystal structure was determined) exhibits the property of interfacial activation, where enhanced activity is observed when the substrate PI is present in an interface compared to monomeric substrate (Lewis et al., 1993). However, other non-substrate lipids such as phosphatidylcholine (PC), phosphatidic acid (PA), and other anionic lipids have an effect on the activity of PI-PLC toward both substrates PI and water-soluble cIP (Zhou et al., 1997). In particular, the presence of PC enhances the catalytic activity of... 

Figure 1 Examples of several bacterial membrane proteins. The outer membrane (OM) of Gram-negative bacteria contains exclusively fS-barrel proteins, and three examples are shown BtuB (PDB ID 1NQF), which is the 22 p-stranded TonB-dependent active transporter for vitamin B 2/ th LamB or maltoporin trimer (PDB ID 1AF6), which is the 18 p-stranded passive sugar transporter and OmpA (PDB ID 1BXW), which is an 8 p-stranded protein that provides structural support for the OM. Proteins in the cytoplasmic membrane (CM) are helical, and three examples are shown the potassium channel KcsA (PDB ID 1BL8), which is a tetramer Sec YEG (PDB ID 1RH5), which forms the protein transport channel in Methanococcus and BtuCD (PDB ID ...

Family 8 contains nine genes, all bacterial, which appear to code for endocellulases utilizing the inverting mechanism. The structure of a family 8 endocellulase, C. thermocellum Cel A, has been determined and it is an (a/a)g barrel similar to those found in families 9 and 48 [35,59]. 

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