Evolutionary binding-site conservation

The X-ray structures of vanadium bromoperoxidases from the red seaweeds Corallina pilulifera and C. officinalis have also been determined and their structures are almost identical. The native structure of these enzymes is dodecameric and the structure is made up of 6 homo-dimers. The secondary stmcture of the chloroperoxidase from the ftmgus Curvularia inaequalis that will be discussed later can be superimposed with the Corallina hromoperoxidase dimer. Many of the a helices of each chloroperoxidase domain are structurally equivalent to the a helices in the Corallina hromoperoxidase dimer. This is in line with the evolutionary relationship between the haloperoxidases that will be discussed later. The disulfide bridges in the enzyme from A. nodosum are not found in the enzyme from Corallina and the two remaining cysteine residues are not involved in disulfide bonds. Additionally, in this enzyme binding sites are present for divalent cations that seem to be necessary to maintain the stmcture of the active site cleft. All the residues directly involved in the binding of vanadate are conserved in the algal bromoperoxidases. ... 

Type II restriction enzymes are prevalent in Archaea and Eubacteria. What can we tell of the evolutionary history of these enzymes Comparison of the amino acid sequences of a variety of type II restriction endonucleases did not reveal significant sequence similarity between most pairs of enzymes. However, a carefiil examination of three-dimensional structures, taking into account the location of the active sites, revealed the presence of a core structure conserved in the different enzymes. This structure includes P strands that contain the aspartate (or, in some cases, glutamate) residues forming the magnesium ion binding sites (Figure 9.44). 

All these data appear to indicate a possible evolutionary process from a common proteic antecesor to two different TRs. To clarify the differences between TRI and TRII, crystal studies were developed, showing that the binding site for the cofactor and the position of the active site residues were well conserved. The substrate binding site was composed of hydrophobic amino acids, the different charges of... 

Key Words Multiple alignment alignment tool evolutionary conservation conserved elements conserved transcription factor binding sites. 

Cytochrome c oxidase is a highly conserved enzyme the three core subunits (I, II and III) encoded by the mitochondrial genome in eukaryotes has high amino acid sequence homology with prokaryotic and eukaryotic species. Detailed analysis of evolutionary conservation of lipid-binding sites in cytochrome c oxidase (Qin et al., 2007) shows that lipid binding sites are specific and... 

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