Barrel domain

Figure 4.4 Schematic diagram of the structure of the a/p-barrel domain of the enzyme methylmalonyl-coenzyme A mutase. Alpha helices are red, and p strands are blue. The inside of the barrel is lined by small hydrophilic side chains (serine and threonine) from the p strands, which creates a hole in the middle where one of the substrate molecules, coenzyme A (green), binds along the axis of the barrel from one end to the other. (Adapted from a computer-generated diagram provided by P. Evans.)...

Figure 4.5 The polypeptide chain of the enzyme pyruvate kinase folds into several domains, one of which is an a/p barrel (red). One of the loop regions in this barrel domain is extended and comprises about 100 amino acid residues that fold into a separate domain (blue) built up from antiparallel P strands. The C-terminal region of about 140 residues forms a third domain (green), which is an open twisted a/p structure.

All known eight-stranded a/p-barrel domains have enzymatic functions that include isomerization of small sugar molecules, oxidation by flavin coenzymes, phosphate transfer, and degradation of sugar polymers. In some of these enzymes the barrel domain comprises the whole subunit of the protein in others the polypeptide chain is longer and forms several additional domains. An enzymatic function in these multidomain subunits, however, is always associated with the barrel domain. 

For example, each subunit of the dimeric glycolytic enzyme triosephos-phate isomerase (see Figure 4.1a) consists of one such barrel domain. The polypeptide chain has 248 residues in which the first p strand of the barrel starts at residue 6 and the last a helix of the barrel ends at residue 246. In contrast, the subunit of the glycolytic enzyme pyruvate kinase (Figure 4.5), which was solved at 2.6 A resolution in the laboratory of Ffilary Muirhead, Bristol University, UK, is folded into four different domains. The polypeptide chain of this cat muscle enzyme has 530 residues. In Figure 4.5, residues 1-42... 

Figure 4.7 Two of the enzymatic activities involved in the biosynthesis of tryptophan in E. coli, phosphoribosyl anthranilate (PRA) isomerase and indoleglycerol phosphate (IGP) synthase, are performed by two separate domains in the polypeptide chain of a bifunctional enzyme. Both these domains are a/p-barrel structures, oriented such that their active sites are on opposite sides of the molecule. The two catalytic reactions are therefore independent of each other. The diagram shows the IGP-synthase domain (residues 48-254) with dark colors and the PRA-isomerase domain with light colors. The a helices are sequentially labeled a-h in both barrel domains. Residue 255 (arrow) is the first residue of the second domain. (Adapted from J.P. Priestle et al., Proc.

Most of the known antiparallel p structures, including the immunoglobulins and a number of different enzymes, have barrels that comprise at least one Greek key motif. An example is 7 crystallin, which has two consecutive Greek key motifs in each of two barrel domains. These four motifs are homologous in terms of both their three-dimensional structure and amino acid sequence and are thus evolutionarily related. 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

Fig. 6. Distribution of the most common folds in selected bacterial, archaeal, and eukaryotic proteomes. The vertical axis shows the fraction of all predicted folds in the respective proteome. Fold name abbreviations FAD/NAD, FAD/NAD(P)-binding Rossman-like domains TIM, TIM-barrel domains SAM-MTR, S-adenosylmethionine-dependent methyltransferases PK, serine-threonine protein kinases PP-Loop, ATP pyrophosphatases. mge, Mycoplasma genitalium rpr, Rickettsiaprowazekii hh x, Borrelia burgdorferi ctr, Chlamydia trachomatis hpy, Helicobacter pylori tma, Thermotoga maritima ssp, Synechocystis sp. mtu, Mycobacterium tuberculosis eco, Escherichia coli mja, Methanococcus jannaschii pho, Pyrococcus horikoshii see, Saccharomyces cerevisiae, cel, Caenorhabditis elegans.

Domain 1 up-and-down fi barrel Domain 2 miscellaneous antiparallel a Domain 3 doubly wound parallel fi sheet... 

Fig. 101. Packing of two 0 barrel domains in the immunoglobulin VL dimer (from Bence-Jones REI) (a) a-carbon stereo, viewed from the sides of the barrels (b) simplified schematic of the barrels as cylinders, viewed as in a (c) a-carbon stereo, viewed from one end of the barrels. The contact between the two domains forms a third barrel in the center.

Rebsam A, Seif I, Gaspar P (2002) Refinement of thalamocortical arbors and emergence of barrel domains in the primary somatosensory cortex a study of normal and monoamine oxidase aknock-out mice. J Neurosci 22 8541-8552... 

Currently there is no experimentally determined three-dimensional structural information available for OSCs, although studies with a related enzyme, squa-lene-hopene cyclase (SC EC 5.4.99.7) have proved informative. SCs are involved in the direct cyclisation of squalene to pentacyclic triterpenoids known as hopanoids, which play an integral role in membrane structure in prokaryotes [ 51 ]. A number of SC genes have been cloned from bacteria [52 - 54]. The SC and OSC enzymes have related predicted amino acid sequences, and so should have similar spatial structures [55]. The crystal structure of recombinant SC from the Gram-positive bacterium Alicyclobacillus acidocaldarius has established that the enzyme is dimeric [55]. Each subunit consists of two a-a barrel domains that assemble to form a central hydrophobic cavity [55,56]. 

Figure 5-40 Structure of a protein known as transcription factor NF-kB bound to its DNA target. Each subunit of the dimeric protein contains two (3 barrel domains. The loops at the ends of the barrels interact with the DNA in the center. From Muller et al.433 Courtesy of Stephen C. Harrison.

This editing mechanism for isoleucyl-tRNA synthetase was demonstrated directly in 1998 by X-ray crystallography on complexes of the enzyme with L-isoleucine and L-valine. Both substrates fit into the ATP-requir-ing synthetic site but neither isoleucine nor isoleucyl-tRNA will fit into the editing site which is located in an adjacent (3-barrel domain.104 105 Proofreading steps based on differing chemical properties as well as size can also be visualized.103 106... 

Ras proteins fulfill their functions by interacting closely with two or more proteins in signaling pathways as described in Section H. Other G proteins have additional domains. The 405-residue EF-Tu from Thermus thermophilus has three domains the C-terminal nucleotide-binding domain and two P-barrel domains following it. A major difference in conformation is observed between forms of the protein with bound... 

Two types of dissimilatory nitrite reductases catalyze step b of Eq. 18-30. Some bacteria use a copper-containing enzyme, which contains a type 1 (blue) copper bound to a (3 barrel domain of one subunit and a type 2 copper at the catalytic center. The type 1 copper is thought to receive electrons from the small copper-containing carrier pseudoazurin (Chapter... 

B major axis near /J-strand 1 M R, M LE are missing final a-helix domains cover the C-terminal end of the barrel domain blocks N-terminus of the barrel mandelate racemase, muconate cycloisomerase, xylose (glucose) isomerase... 

Fig. 13. Superposition of a/ji barrel domains of MR (white/red), MLE I (blue/red), enolase (yellow/red). Red coloring represents most similar regions among each pairwise comparison as described in the text.

Fig. 12. a/fi barrel domain of MR (based on Protein Data Bank entry 1 mnr). Important active site residues and the associated secondary structure elements are labeled and designated with arrows. From Babbitt and Gerlt (1997, Figure 1, p. 30592). 

Huang, X.L., Catignani, G.L., and Swaisgood, H.E. 1996. Improved emulsifying properties of the (3-barrel domain peptides obtained by membrane-fractionation of a limited tryptic hydrolysate of (3-lactoglobulin. J. Agric. Food Chem. 44, 3437-3443. 

Jespersen, H. M., MacGregor, A., Henrissat, B., Sierks, M. R., and Svensson, B. 1993. Starch-and glycogen-debranching and branching enzymes prediction of structural features of the catalytic (/S/a)g-barrel domain and evolutionary relationship to other amylolytic enzymes. J. Protein Chem. 12,781-805. 

Like transketolase, transaldolase (TA, E.C. 2.2.1.2) is an enzyme in the oxidative pentose phosphate pathway. TA is a class one lyase that operates through a Schiff-base intermediate and catalyzes the transfer of the C(l)-C(3) aldol unit from D-sedoheptulose 7-phosphate to glyceraldehyde-3-phosphate (G3P) to produce D-Fru 6-P and D-erythrose 4-phosphate (Scheme 5.59). TA from human as well as microbial sources have been cloned.110 111 The crystal structure of the E. coliu and human112 transaldolases have been reported and its similarity to the aldolases is apparent, since it consists of an eight-stranded (o /(3)s or TIM barrel domain as is common to the aldolases. As well, the active site lysine residue that forms a Schiff base with the substrate was identified.14112 Thus, both structurally and mechanistically it is related to the type I class of aldolases. 

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