Residue location

In higher eukaiyotes, most of the chromosomal DNA carries 5-methyl-cytidine residues located in CpG sequence motives. There is a close correlation between transcriptional inactivation and methylation. On the other hand, considerable evidence shows that regions of DNA that are actively engaged in transcription lack 5-methyl-cytidine nucleotides in CpG motivs. Hence DNA methylation is a means how cells regulate gene expression. DNA methylation which is catalyzed by DNA methyltransferases is the best characterized epigenetic mechanism. 

The primary site of action of OPs is AChE, with which they interact as suicide substrates (see also Section 10.2.2 and Chapter 2, Figure 2.9). Similar to other B-type esterases, AChE has a reactive serine residue located at its active site, and the serine hydroxyl is phosphorylated by organophosphates. Phosphorylation causes loss of AChE activity and, at best, the phosphorylated enzyme reactivates only slowly. The rate of reactivation of the phosphorylated enzyme depends on the nature of the X groups, being relatively rapid with methoxy groups (tso 1-2 h), but slower with larger... 

DNA sequence indicated that AMDase contains four cysteine residues located at 101, 148, 171 and 188 from amino terminal (Eig. 9). At least one of these four is estimated to play an essential role in the decarboxylation. The most effective way to determine which Cys is responsible to enzyme activity will be site-directed mutagenesis. To determine which amino acid should be introduced in place of active Cys, its role was estimated as illustrated in Eig. 13. One possibility is that... 

The slow and fast isoenzymes of Ca -ATPase contain 13 and 12 histidine residues, respectively [8]. Only seven of these occur in identical positions in the two isoenzymes these correspond to His51, 190, 278, 284, 682, 871 and 943 in the sequence of the slow -ATPase. The stretch of five histidine residues, located in the slow isoenzyme at positions 396, 406, 526, 566 and 576, have no counterparts in the fast Ca " -ATPase. None of the highly conserved sequences of the Ca -ATPase appear to contain histidine. This still leaves the possibility open for the direct or indirect involvement of histidine residues in ATP hydrolysis and Ca " transport. Such a role is suggested ... 

However, diffusion of the reactive QM out of the enzyme active site is a major concern. For instance, a 2-acyloxy-5-nitrobenzylchloride does not modify any nucleophilic residue located within the enzyme active site but becomes attached to a tryptophan residue proximal to the active site of chymotrypsin or papain.23,24 The lack of inactivation could also be due to other factors the unmasked QM being poorly electrophilic, active site residues not being nucleophilic enough, or the covalent adduct being unstable. Cyclized acyloxybenzyl molecules of type a could well overcome the diffusion problem. They will retain both the electrophilic hydroxybenzyl species b, and then the tethered QM, in the active site throughout the lifetime of the acyl-enzyme (Scheme 11.1). This reasoning led us to synthesize functionalized... 

Most of the G-protein-coupled receptors are homologous with rhodopsin however, other quantitatively minor families as well as some individual receptors do not share any of the structural features common to the rhodopsin family (Figure 2.3). The most dominant of these are the glucagon/VIP/caldtonin receptor family, or family B (which has approximately 65 members), and the metabotropic glutamate receptor family, or family C (which has approximately 15 members), as well as the frizzled/smoothened family of receptors. Thus, the only structural feature that all G-protein-coupled receptors have in common is the seven-transmembrane helical bundle. Nevertheless, most non-rhodopsin-like receptors do have certain minor structural features in common with the rhodopsin-like receptors — for example, a disulfide bridge between the top of TM-III and the middle of extracellular loop-3, and a cluster of basic residues located just below TM-VI. 

As described in more detail below, agonist binding will lead to signaling as well as phosphorylation of Ser and Thr residues, especially, but also, in selected cases, Tyr residues located in intracellular loop-3 and in the C-terminal extension. This post-translational modification alters the affinity of the receptor for various intracellular proteins, including arrestin, which sterically prevents further G-protein binding and functions as an adaptor protein. Also, interaction with other types of scaffolding proteins such as PSD-95-like proteins, is influenced by the phosphorylation state of the receptor. 

Structural and functional evidence clearly demonstrates that family C receptors function as dimers, either as homodimers or as heterodimers. The metabotropic glutamate receptors and the calcium sensors, as discussed in Section 2.6.1, are found as covalently connected dimers in which there is a disulfide bridge between a Cys residue located in a loop in the N-terminal extracellular domain of each monomer. This disulfide bridge apparently serves only to hold the monomers in close proximity, as the loop is so unstructured that it does not resolve in the x-ray structure. 

In principle, RTK autophosphorylation could occur in cis (within a receptor monomer) or in trans (between two receptors in a dimer). In the first case, ligand binding would cause a change in receptor conformation that would facilitate c/ s-autophosphorylation of tyrosine residues located within or outside the PTK domain. In the second case, no conformational change must occur upon dimerization. The simple proximity effect would provide sufficient opportunity for trans-phosphorylation of tyrosines in the cytoplasmic domain by a second RTK. 

The crystallographic structure of rubredoxin from Clostridium pasteurianum at 2.5 A, a resolution sufficient to reveal the sequence of several of the bulky amino acid side chains, shows the iron coordinated to two pairs of cysteine residues located rather near the termini of the polypeptide chain (Fig. 1). A related rubredoxin, with a three times larger molecular weight, from Pseudomonas oleovorans is believed to bind iron in a similar fashion. This conclusion is based on physical probes, especially electron paramagnetic resonance spectroscopy, all of which indicate that the iron is in each case situated in a highly similar environment however, the proteins display some specificity in catalytic function. 

A significant increase in J (0) is observed for the NH resonances of some residues located in the A and G helices of the folded protein (upper panel of Fig. 8) and is associated with fluctuations on a /jls-ms time scale that probably arise from transient, native-like contacts between these distant regions of the polypeptide chain. These results have been confirmed... 

The assignment of the 13C NMR peaks of Pro 50, 91, and 186 from [l-13C]Pro-labelled bR is performed with reference to those of P50G, P91G, and PI 86A mutants, to reveal the dynamic features of the Pro residues located at the possible kinked portions in the inner part of the TM a-helices, as demonstrated in Figure 28A, top trace. For this purpose, selection of these three peaks was made among seven resolved peaks by use of Mn2+ induced suppression of peaks from residues located near the surface due to accelerated spin-spin relaxation times, as shown in Figure 28A, middle and bottom traces. 

The solution structures of Raf-, Rif-, and RalGDS-RBD were solved and, in addition, NMR spectroscopy was used to probe the interaction with Ras [211, 213,219]. Only the RBD was labeled with 15N and the shifting of distinct cross peaks (HSQC spectra) due to binding of Ras allowed one to identify the binding surface on the RBD. Consistent with X-ray structures of the complexes (see above) in both Raf and RalGDS, amino acid residues located in (31 and (32 and the C-terminal part of al are involved in the interaction with Ras. 

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