P Sandwich

Fig. 10. Sequences (see Table 1) of betabeUins. In each case, only one-half of the P-sandwich is shown. The dimer is formed from identical monomeric sets of four P-strands. In the pattern sequence, e is for end, p is for polar residue, n is for nonpolar residue, and t and r are for turn residues. Lower case f is iodophenyialanine lower case a, d, k, and p are the D-amino acid forms of alanine, aspartic acid, lysine, and proline, respectively B is P-alanine (2,53,60,61).

The apical domain (blue), which is a p sandwich flanked by a helices, is formed by the middle region of the polypeptide chain. The two linker regions between the equatorial and the apical domains form a small infermediate domain (purple) comprising three a helices. 

TFIIA also has two domains, one of which is a four-helix bundle and the other an antiparallel p sandwich. The p sandwich interacts with the N-termi-nal half of TBP and thus positions TFIIA on the other side of the complex compared with TFIIB. This domain also interacts with phosphates and sugars of DNA upstream of the TATA box. Tbe four-helix bundle domain makes no contact with DNA or TBP and is far removed from the position of TFIIB. 

The eight-stranded P cylinder of plastocyanin (Fig. 2-16A) is somewhat flattened and can also be regarded as a P sandwich.116118 However, the P barrel of triose phosphate isomerase (see Fig. 2-28) is surrounded by eight a helices which provide additional stability and a high symmetry. Bacterial outer membranes contain pores created by very large P cylinders within proteins called porins.119120 Tire one shown in Fig. 8-20 has 16 strands. 

CPMV particles have an icosahedral symmetry with a diameter of approximately 28 nm (Figure 9.2), the protein shell of the capsid is about 3.9nm thick [72], The structure of CPMV is known to near-atomic resolution (Figure 9.3) [73], The virions are formed by 60 copies of two different types of coat proteins, the small (S) subunit and the large (L) subunit. The S subunit (213 amino acids) folds into one jelly roll P-sandwich, and the L subunit (374 amino acids) folds into two jelly roll P-sandwich domains. The three domains form the asymmetric unit and are arranged in a similar surface lattice to T = 3 viruses, except they have different polypeptide sequences therefore the particle structure is described as a pseudo T = 3 or P = 3 symmetry [74]. 

The crystal structure of cucumber basic blue protein has now been refined to 3.0 A resolution (Adman, 1985). The protein consists of eight strands, only five of which form a P-sandwich and the protein has less P-sheet character than plastocyanin or azurin. The ligands to copper are provided by the side chains of His-39, Cys-79, His-84 and Met-89. The copper site has the N2SS coordination seen in plastocyanin. The imidazole rings of the His-39 and His-94 residues are exposed to the solvent providing a likely entry site for electon transfer to the copper centre. 

Domain III has also been shown to participate in ion channel activity. CiylAa and Cry3A show highly structural similarity in domain III. On the inner (focing domain I) sheet of the p-sandwich, four arginines on foe highly conserved strand pi7 participate in a network of charge interactions [31]. In CiylAa, substitution of foe central arginines in... 

Finally, in Plate 21, the structure of the yeast TFIIA-TBP-DNA complex is shown. TFIIA interacts with TBP and the TFIID complex and stimulates transcription of the Pol II gene.29-32 TFIIA has two characteristic structural motife. One is a six-stranded (i-sand-wich, the other is a left-handed four-helix bundle. The P-sandwich domain of TFUA is alone responsible for all of the interactions with the DNA, whereas its helix-bundle domain projects away and is free to interact with signal-responsive transcription factors. These interactions are important for regulation of transcription. Little conformational change occurs in TBP when it binds to TFIIA. The main difference between the TFIIA-TPB complex and the TFIIB-TBP complex is that TFIIA binds upstream of the TATA box, away from the transcriptional start site, whereas TFIIB binds downstream of the TATA box. Moreover, TFIIB is positioned on the side opposite to TFIIA. 

Fig. 10.3 The C-terminal domain (residues 319-552) of human SMAD 4 at 2.5 A resolution It is a three-helix bundle attached to a P-sandwich scaffold (compare with the STAT 4 structure in Fig. 10,4). (Reproduced with permission of the authors and Nature from data in ref. 35, and the data availabie in the protein databanks.)...

In addition, there are two pairs of P hairpin arms which connect the subunits. One arm from each subunit lies across the upper surface of the P sandwich domain whilst the other arm from each subunit lies towards the bottom of the cap and penetrates deeply into the other subunit providing what appears to be a link between the active sites (Figure 11b). 

Clarke, J., Cota, E., Fowler, S.B., Hamill, S.J. Folding studies of immunoglobulin-like p-sandwich proteins suggest that they share a common folding pathway. Structure 1999, 7,1145-53. 

The chemokine (CK) subfamily of cytokines with a general conformation of an open-face p-sandwich with a C-terminai a-helical segment, divided into three major subgroups based on the amino acid sequence around the conserved cysteine residues. 

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