Two-domain organization

Protein phosphatase 2A phosphatase activator, also known as Phosphotyrosyl phosphatase activator, PTPA, a conserved protein from yeast to humans. Its enzymatic activity as a peptidyl prolyl cis/trans isomerase has recently been identified, making it the fourth family of the enzyme class EC 5.2.1.8. Its isomerase activity can be stimulated by Mg /ATP. The three-dimensional structure of PTPA does not resemble those of other families of peptidyl prolyl cis/trans isomerases as an aU-helical fold dominates the two-domain organization of the enzyme. In the enzyme-peptide substrate complex, the peptide binds at the interface of a peptide-induced PTPA dimer. Apparently, protein phosphatase 2A activation and peptidyl prolyl cis/trans isomerase activity of PTPA are functionally linked in vitro [N. LeuUiot et al., J. Mol. Cell 2006, 23, 413]. 

The most common group of fimbrial adhesins of Escherichia coli occurs at the edge of their fimbriae and have a two-domain organization. The most external N-terminal domain is a lectin, whereas the C-terminal pilin connects to the rest of the fimbrius. In Fig. 5, the lectin domains from E. coli adhesins that have been crystallised in complex with a specific glycan sequence are displayed, with the exception of CfaE that was only crystallized in its glycan-free form. PapGII (Pap for pyelonephritis associated pili) is the fimbrial adhesin at the tip of P fimbriae from... 

Figure 2.19 Organization of polypeptide chains into domains. Small protein molecules like the epidermal growth factor, EGF, comprise only one domain. Others, like the serine proteinase chymotrypsin, are arranged in two domains that are required to form a functional unit (see Chapter 11). Many of the proteins that are involved in blood coagulation and fibrinolysis, such as urokinase, factor IX, and plasminogen, have long polypeptide chains that comprise different combinations of domains homologous to EGF and serine proteinases and, in addition, calcium-binding domains and Kringle domains.

Figure 13.6 Schematic diagram of Go. from transducin with a bound GTP analog. The polypeptide chain is organized Into two domains a catalytic domain (light red) with a structure similar to Ras, and a helical domain (green) which is an Insert in the loop between al and P2. There are three switch regions (violet) that have different conformations in the different catalytic states of Go.. The GTP analog (brown) Is bound to the catalytic domain in a cleft between the two domains. (Adapted from J. Noel et al.. Nature 366 654-663, 1993.)...

Methylenetetrahydrofolate reductase (MTHFR) catalyzes the NAD(P)H-dependent reduction of 5,10-methylenetetrahydrofolate (CH2-THF) to 5-methyltetrahydrofolate (CH3-THF). CH3-THF then serves as a methyl donor for the synthesis of methionine. The MTHFR proteins and genes from mammalian liver and E. coli have been characterized,12"15 and MTHFR genes have been identified in S. cerevisiae16 and other organisms. The MTHFR of E. coli (MetF) is a homotetramer of 33-kDa subunits that prefers NADH as reductant,12 whereas mammalian MTHFRs are homodimers of 77-kDa subunits that prefer NADPH and are allosterically inhibited by AdoMet.13,14 Mammalian MTHFRs have a two-domain structure the amino-terminal domain shows 30% sequence identity to E. coli MetF, and is catalytic the carboxyterminal domain has been implicated in AdoMet-mediated inhibition of enzyme activity.13,14... 

The MTHFRs of Arabidopsis and maize have recently been cloned by genomics-based approaches, based on homology with the enzymes from other organisms.17 Like mammalian MTHFRs, the plant enzymes were found to be homodimers of two-domain subunits that are homologous to the mammalian enzymes throughout both domains. However, when the recombinant plant proteins were expressed in yeast, they were found to differ radically from the mammalian MTHFRs in both their pyridine nucleotide preference and their regulatory properties plant enzymes prefer NADH to NADPH, and they are insensitive to AdoMet.17... 

Fig. 65. The dumbbell domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains.

Methanogenic organisms are placed among the archaea, and they differ significantly from the other two domains of life, the eukarya and bacteria. The... 

Group I intron phosphotransesterification reactions are carried out by a conserved active site that contains a set of imperfect double helices named PI through P9. (See Figure 6.4.) P1-P9 helices are organized into three domains P1-P2, P4-P6, and P3-P9. Specifically, the Tetrahymena thermophila intron contains two sets of coaxially stacked helices that overlap to create the active site. These helices reside in two domains of approximately equal size P4-P6 and P3-P9. P domains are defined as base-paired regions, whereas J domains... 

Fig. 1. Domain organization of selected remodeling polypeptides. The translocase/ATPase domain in InoSO is split into two regions [60].

Fe atoms. It had been anticipated that the c-type cytochrome center would have His/Met coordination, but His/His is observed. The former is the more usual coordination, especially at the high potential end E° > +200 mV) ofthe typical bacterial electron transfer chain to which the nitrite reductase is connected (Fig. 2) (7). The second curious feature is that the di heme iron is also six-coordinate thus, the enzyme does not offer a substrate-binding site at either heme. In addition to an expected axial histidine ligand there was an axial tyrosine (residue 25) ligand to the d heme (Fig. 4a). Each monomer is organized into two domains. 

Detailed pictures of the iron-binding sites in transferrins have been provided by the crystal structures of lactoferrin (Anderson et ai, 1987, 1989 Baker etai, 1987) and serum transferrin (Bailey etal., 1988). Each structure is organized into two lobes of similar structure (the amino- and carboxy-terminal lobes) that exhibit internal sequence homology. Each lobe, in turn, is organized into two domains separated by a cleft (Fig. 3 and 10). The domains have similar folding patterns of the a//3 type. One iron site is present in each lobe, which occupies equivalent positions in the interdomain cleft. The same sets of residues serve as iron ligands to the two sites two tyrosines, one histidine, and one aspartate. Additional extra density completes the octahedral coordination of the iron and presumably corresponds to an anion and/or bound water. The iron sites are buried about 10 A below the protein surface and are inaccessible to solvent. 

The protein is organized into two domains, each able to bind a cluster of metal ions via thiolate side chains. 

The dumbbell domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains. (Copyright 1994 by the Scripps Research Institute/Molecular Graphics Images by Michael Pique using software by Yng Chen, Michael Connolly, Michael Carson, Alex Shah, and AVS, Inc. Visualization advice by Holly Miller, Wake Forest University Medical Center.)... 

Indeed, homologous regions of all of the a-actinin protein domains can be found within the sequences of a- and /3-spectrin. For example, the amino and carboxy terminal regions of a-actinin resemble the N-terminus of /3-spectrin and the C-terminus of a-spectrin, respectively (Byers et al, 1989 Dubreuil et al, 1989). Phylogenetic analysis shows a common ancestor for the first repeat of a-actinin and the first repeat of /3-spectrin. Similarly, each of the remaining repeats in a-actinin (2—4) correspond to repeats 1 and 2 of /3-spectrin and repeats 19 and 20 of a-spectrin respectively (Fig. 2). This may have relevance for the function of these repeats in the dimerization of these proteins (Pascual et al, 1997). It is the similarity between these regions of a-actinin, the spectrins, and the simpler domain organization of a-actinin that have led to the hypothesis that these two protein families have evolved from an a-actinin-like precursor. 

Figure 13.3 Domain organization of Tap. Human Tap is a 619-amino acids protein. The minimal CTE-binding domain is composed of two globular sub-domains (the ribonucleprotein or RNP domain and the leucine-rich repeat or LRR) and a flexible N-terminal region. Also shown is the localization of the C-terminal nucleocytoplasmic shuttling domain, the cargo-binding domain, and the NTF2-like domain that exhibits pi5 binding activity.

Figure 10.6 shows the alignment of amino acid sequences of Fe- and Mn-SODs so far determined. The amino acid sequences of Fe-SODs show a high degree of homology with those of Mn-SODs. His-26, His-73, Asp-156, and His-16049) in E. coli Fe-SOD serve as the metal ligands (Fig. 10.7) and are conserved in both Mn- and Fe-SODs from other organisms (Fig. 10.6). The three-dimensional structures have been determined for Mn-SODs from Thermus thermophilus HB8 (2.4 A)50) and Bacillus stearothermophilus (2.4 A)5I,52) and for Fe-SODs from E. coli (3.lA)53) and Pseudomonas ovalis (2.9 A).54) The polypeptide chain of the monomer of Mn-SOD is composed of two domains one has an all-a structure and the other an a) ft structure, with the Mn ion bound between them (Fig. 10.8).

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