Structure conserved cysteine residues

The Sema domain consisting of about 500 amino acids is characterized by highly conserved cysteine residues that form intramolecular disulfide bonds. Crystal structures have revealed that the Sema domain folds in the manner of the (3 propeller topology which is also found in integrins or the low-density lipoprotein (LDL) receptors. Sema domains are found in semaphorins, plexins and in the receptor tyrosine kinases Met and Ron. 

Early mutational studies of the Rieske protein from 6ci complexes have been performed with the intention of identifying the ligands of the Rieske cluster. These studies have shown that the four conserved cysteine residues as well as the two conserved histidine residues are essential for the insertion of the [2Fe-2S] cluster (44, 45). Small amounts of a Rieske cluster with altered properties were obtained in Rhodobacter capsulatus when the second cysteine in the cluster binding loop II (Cys 155, corresponding to Cys 160 in the bovine ISF) was replaced by serine (45). The fact that all four cysteine residues are essential in Rieske clusters from be complexes, but that only two cysteines are conserved in Rieske-type clusters, led to the suggestion that the Rieske protein may contain a disulfide bridge the disulfide bridge was finally shown to exist in the X-ray structure (9). 

Details regarding structural/functional differences among chemokines and their receptors are discussed elsewhere in this volume. Briefly, chemokines (and their cognate receptors) consist of four main classes (CC, CXC, CX3C and C) based on the number and spacing of at least four conserved cysteine residues (Murphy 2002). 

Figure 12.3 NMR structure of reduced CopZ. Schematic representation of the NMR-derived structure of reduced CopZ, displaying the conserved cysteine residues a-helix (yellow), a-sheet (blue), loop or turn (red). Reprinted from Harrison et ah, 2000. Copyright (2000), with permission from Elsevier Science. 

Although the occurrence of six conserved cysteine residues, the spacing patterns of these residues, and possibly the pattern of disulfide structures are hallmarks of OBPs, the six-cysteine criterion alone is not sufficient to classify a certain protein as an olfactory protein [ 16]. It is important to demonstrate that an OBP is expressed only (or predominantly) in olfactory tissues. Evidence for their ability to bind odorants is also desirable, but not sine qua non. One of these criteria alone would not be enough to define a given protein as an OBP. For example, bovine serum albumin (BSA) binds to insect pheromones (Leal, unpublished data) and yet it is not an OBP because it not expressed in insect olfactory tissues. Conversely, a protein specific to antennae is not necessarily an OBP. There are other proteins that may be expressed in antennae but not in control tissues. Non-OBPs specifically accumulated in insect antennae have been previously detected (Ishida and Leal, unpublished data). Also, a glu-tathione-S-transferase has been reported to be expressed specifically in antennae of M. sexta [52]. 

Metallothioneins are small proteins of about 60 amino acids (20 of which are conserved cysteine residues) that bind copper, zinc, and cadmium (Melis etal, 1983 Furey etal, 1986). Solution structures have been elucidated by NMR, showing the coordination schemes (Schultze et ai, 1988). 

Crystals of pronase-released heads of the N2 human strains of A/Tokyo/3/67 [44] and A/RI/5+/57 were used for an x-ray structure determination. The x-ray 3-dimensional molecular structure of neuraminidase heads was determined [45] for these two N2 subtypes by a novel technique of molecular electron density averaging from two different crystal systems, using a combination of multiple isomorphous replacement and noncrystallographic symmetry averaging. The structure of A/Tokyo/3/67 N2 has been refined [46] to 2.2 A as has the structures of two avian N9 subtypes [47-49]. Three influenza type structures [50] have also been determined and found to have an identical fold with 60 residues (including 16 conserved cysteine residues) being invariant. Bacterial sialidases from salmonella [51] and cholera [52] have homologous structures to influenza neuraminidase, but few of the residues are structurally invariant. 

Fig. 1 The structure of a-LTX. (a) Schematic of a-LTX processing in the venom gland, (b) Primary and domain structure. The numbered boxes, ankyrin repeats (ARs). Grey, imperfect repeats C, conserved cysteines residues in the N-terminal domain open arrowhead, insert in the mutant a-LTXN4C. Protein domains identified from the 3D structure (Orlova et al. 2000) are delimited below, (c) 3D reconstructions of the a-LTX monomer, dimer and tetramer, viewed from the top and side. The monomer has been computationally extracted from the experimentally determined tetramer structure. Left-most image, a scheme of the monomer, with the domains designated by different shades of grey. Filled arrowhead, strong association of the head domains in the dimer.

Metallothioneins are evolutionarily conserved in that they contain a high cysteine content and lack of aromatic amino acids. However, few invertebrate MTs have been characterized, and these can exhibit wide variation in noncysteine amino acid residues. Initially, MTs were classified according to their structural characteristics. Class I MTs consist of polypeptides with highly conserved cysteine residue sequences and closely resemble the equine renal MT. Mammalian MTs consist of 61-68 amino acids residues and the sequence is highly conserved with respect to the position of the cysteine residues (e.g., cys-x-cys, cys-x-y-cys, and cys-cys sequences, where x and y are noncysteine, non-aromatic amino acids). Class II MTs have less conserved cysteine residues and are distantly related to mammalian MTs. Class III MTs are defined as atypical and consist of enzymatically synthesized peptides such as phy-tochelatins and cadystins. This former classification scheme has been replaced by a more complex system to include the increasing number of identified isoforms. 

Although traditionally found in tRNA, m U is also seen in ribosomal RNA (rRNA). The enzyme RumA catalyzes the site-specific methylation of U1939 in rRNA, and is distinguished from enzymes in the RUMT family in that it contains sequence homology with the putative RNA-binding TRAM domain in the N-terminus. With a crystal structure determined to 1.95 A, four conserved cysteine residues were found in... 

Several structures of LipDHs have been determined by X-ray diffraction, including a structure from Pseudomonas putida, solved to 2.45 A resolution. The enzyme from P. putida consists of two identical subunits — as do all LipDHs — each of molecular mass 48 159 Da, and is only active as a dimer. Each subunit contains four domains. The largest domain binds FAD and is in contact with the other three domains an NAD-binding domain, a central domain, and an interface domain. The active site of one subunit of LipDH is shown in Figure 7. In addition to the FAD cofactor, it contains the disulfide bond formed by conserved cysteine residues 43 and 48, as well as Tyrl81, which covers the NAD -binding pocket in the absence of the pyridine cofactor,... 

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