Extensive sequence conservation

When a protein exhibits extensive sequence similarity to a characterized protein and/or has the same conserved regions, then the label probable is used in the DE line. It is normally followed by the full name of a protein from the same family that it matches. Example ... 

The N-terminus of riboflavin synthases from eubacteria, fungi, and plants is marked by an extraordinary degree of sequence conservation. The canonical amino acid sequence is MFTG, and no N-terminal extensions beyond that motif are known. The replacement of the phenylalanine residue by any amino acid except tyrosine nullifies the catalytic activity of the protein. ... 

The SOD molecule exerts an extensive surface topography of sequence-conserved residues, suggesting that this invariance is critical to the enzymatic function Two pits are seen, forming specific binding sides in the narrowest part of the active-site channel floor. One pit (the Cu-site) is formed by the exposed surface of the Cu(ll) and parts of His-61, His-118, Thr-135 and Arg-141. The adjacent pit (the water-site) is formed by parts of the exposed surface of Thr-135, Gly-136, Ala-138, Gly-139 and Cu-ligands His-44 and His-118. Oj" fit the Cu-site surface with one oxygen bound to the Cu and the other H-bonded to Arg-141. Both active-site channel pits contain highly ordered water molecules. 

First isolated from D. desulfuricans (28), desulfoferrodoxin (Dfe) was also isolated from D. vulgaris (29). D is a 28-kDa homodimer that contains two monomeric iron centers per protein. These iron centers were extensively characterized by UV/visible, EPR, resonance Raman, and Mossbauer spectroscopies (30). The data obtained were consistent with the presence of one Dx-like center (center I) and another monomeric iron center with higher coordination number (penta or hexacoordinate), with 0/N ligands and one or two cysteine residues (center II). Comparison of known Dfx sequences led to the conclusion that only five cysteines were conserved, and that only one of them could be a ligand of center II (31). 

The similarity of the primary structure of different sea snake venoms has already been discussed. Postsynaptic neurotoxins from Elapidae venom have been extensively studied. Elapidae include well-known snakes such as cobra, krait, mambas, coral snakes, and all Australian snakes. Like sea snake toxins, Elapidae toxins can also be grouped into short-chain (Type I) and long-chain (Type II) toxins. Moreover, two types of neurotoxins are also similar to cardiotoxins, especially in the positions of disulfide bonds. However, amino acid sequences between cardiotoxins and sea snake and Elapidae neurotoxins are quite different. In comparing the sequence of sea snake and Elapidae neurotoxins, there is a considerable conservation in amino acid sequence, but the difference is greater than among the various sea snake toxins. 

An extensive analysis of the best IRP-1 binding sequences (from a pool of 16 384 different IRE variants) showed that the selected consensus corresponded exactly to the phylogenetically conserved IRE motif (Henderson et ah, 1994). A certain number of single or double mutations was tolerated at virtually every permuted position. 

Studies on the bacterial type 1 protein azurin have been extensive. Ten different azurin amino-acid sequences have been determined with 47 out of 129 residues (Mf 14,(XX)) conserved. Reduction potentials are in the range 280 339 mV at... 

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

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