Invariant residues

Arrows denote p strands. Colored columns correspond to the five almost Invariant residues described in the text and shown in Figure 13.14. 

Figure 13.14 (a) Schematic diagram of the main chain and four almost invariant residues of the fourth WD repeat of Gp from transducin. The view is roughly perpendicular to the central tunnel and the plane of the sheet. The red stripes denote hydrogen bonds, (b) Schematic view of two WD repeats illustrating the structural relationships between two consecutive repeats. The first repeat is brown and the second repeat is orange. The positions of the four almost invariant residues in the first repeat are circled. (Adapted from J. Sondek et al., Nature 379 369-374, 1996.)... 

The electron transport protein, cytochrome c, found in the mitochondria of all eukaryotic organisms, provides the best-studied example of homology. The polypeptide chain of cytochrome c from most species contains slightly more than 100 amino acids and has a molecular weight of about 12.5 kD. Amino acid sequencing of cytochrome c from more than 40 different species has revealed that there are 28 positions in the polypeptide chain where the same amino acid residues are always found (Figure 5.27). These invariant residues apparently serve roles crucial to the biological function of this protein, and thus substitutions of other amino acids at these positions cannot be tolerated. 

Figure 4. Alignment of PelZ and PelC amino acid sequences. The vertical lines indicate identical amino acids and the two points indicate homologous amino acids. The bold letters correspond to the residues probably involved in Ca + binding or catalytic function(s). The two aspartate residues probably involved in Ca binding are indicated with an asterisk. The invariant residues, probably involved in PGA cleavage, are indicated with an open circle. The folding in p-sheets is characterised by the underlined amino acids. Double underlining of PelZ residues is deduced from Chou Fasman and Robson Gamier folding predictions.

Earlier suggestions that the two uncoordinated and invariant residues His35 (inaccessible to solvent and covered by polypeptide) and His83 (remote and 13 A from Cu) are, from effects of [H ] on rate constants (and related pKg values), sites for electron transfer may require some re-examination. Thus, it has been demonstrated in plastocyanin studies [50] that a surface protonation can influence the reduction potential at the active site, in which case its effect is transmitted to all reaction sites. In other words, an effect of protonation on rate constants need not necessarily imply that the reaction occurs at the site of protonation. His35 is thought to be involved in pH-dependent transitions between active and inactive forms of reduced azurin [53]. The proximity of... 

A murine SIP phosphatase gene, which encodes a 430 amino acid (47.7kDa) protein, has recently been cloned (Mandala et al, 2000). This enzyme bears similarity to a family of lipid phosphate phosphatases (LPPs) (Brindley and Waggoner, 1998) in that it has invariant residues within the three domains of the common predicted catalytic site ((K-X6-RP)-Xu.37-(S-X-H)-X4o.46-(R-Xs-H-X3-D)) although the spacing between the domains differs from the LPPs. In contrast to LPPs, SIP phosphatase is highly... 

Away from the binding pocket, another interesting feature occurs. Invariant residues Lysl4 and Tyr82 occupy entirely new positions in... 

NP2. In particular, Tyr82 flips from outside the protein in NP1/NP4, where it contacts bulk solvent, to inside the protein in NP2, where it hydrogen bonds to Glu55 (110). Thus, modeling the NP2 structure based on those of NPl and NP4, and, as is normally done, keeping the invariant residues structurally conserved, would lead to errors. Structures of protein families such as the nitrophorins therefore provide key information for the future improvement of structure prediction and structural genomics. 

Fig. (4). The primary structures of enod40 peptides. Enod40 peptides are compared from legumes with determinate nodules (a), legumes with indeterminate nodules (b), and non-legumes (c). Gaps (-) were introduce to optimize the alignment. The invariant residues are shown in bold face. The figure was modified after [79],...

Invariant residues in the a and chains of mammalian hemoglobin. The blue dots, indicating the positions of invariant residues, line the heme pockets as well as the crucial a j32 interface. The invariant residues have been found in about 60 species. There are 43 invariant positions in the hemoglobin molecule. (Illustration copyright by Irving Geis. Reprinted by permission.)... 

Table 5.1 Roles of Invariant Residues with Known Functions in Aspartate Aminotransferase...

In other studies, Wain-Hobson and co-workers have selected active variants of dihydrofolate reductase (DHFR, 78 a.a.) from hypermutated libraries (Martinez et al., 1996). Amino acid substitutions were found in all but six residues. Three rounds of mutation and selection led to the isolation of DHFR mutants in which 22% of the amino acids had been substituted. Finally, Palzkill and co-workers have carried out a very systematic mutagenesis of nearly all codons in /1-lactamase (Huang et al., 1996). In this case 43 out of 263 residues were found to not tolerate amino acid substitutions. For DHFR and /8-lactamase, the two enzymes that have been subjected to systematic mutagenesis of nearly every residue, the fraction of invariable residues was roughly of the same order (9% and 16%, respectively). 

Fig. 3. Periplasmic pilus chaperone consensus sequence. Amino acid sequence of the PapD chaperone (top line) and consensus sequence derived from the comparison of twelve chaperones (second line). Amino acids are indicated using the one-letter code. In the consensus sequence, a letter shows a residue that is present in at least eight out of twelve sequences, an asterisk designates an invariant residue, and a box shows a position with a hydrophobic residue in all twelve periplasmic chaperones. The arrows underneath the sequence represent the /3 strands found in the PapD structure.

The phosphotyrosyl binding site of a SH2 domain has two parts. A conserved pocket binds the pTyr. This pocket contains only one crucial invariant residue, an arginine, which forms hydrogen bonds with two oxygens of the... 

Of importance to the RTF, is the occurrence of the invariant residue, Tyr356, in the flexible C-terminal domain of R2. We have suggested that Tyr356 connects the H-bonded arrays of Rl and R2, by making H-bonds directly or indirectly to Trp48 in R2 and to Tyr731 in Rl (Sj"berg, 1997 ... 

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