Phylogenetic sequence homology

Under normal conditions, small blue proteins are monomeric. Their molecular masses range from 10 to 22 kD the corresponding chain lengths vary from 97 to 139 amino acids. Sequence homologies allow small blue proteins to be divided into five group according to their phylogenetic relationship ... 

Nitrite reductase catalyses the reduction of NOj to NO. The enzyme s native state is that of a homotrimer. The monomers have two domains (domain 1 and 2) which show clear sequence homology to type 1 copper proteins [272], Thus, a phylogenetic relationship can be assumed for not only type 1 copper proteins but also for the domains themselves. Domain 1 of nitrite reductase contains type 1 copper, whereas a change in the copper-binding center of domain 2 resulted in its switch from a type 1 to a type 2 copper center. A similar switch from a type 1 to a type 2 copper center may be observed in the development of blue oxidases. 

Sequence homologies are low within type 2 copper proteins. While similarities exist in protein folding or in the structure of the copper centers, they are not based on phylogenetic homologies in amino acid sequence. These similarities are solely the result of separate proteins evolving and adapting to similar functions. In contrast to type 1 copper centers, type 2 copper proteins developed primarily by convergent evolution. 

A phylogenetic relationship may be assumed for amine oxidase and diamine oxidase which shows distinct sequence homologies in their C-terminal regions [128]. Lysyl oxidase is not related to the other amine oxidases as it does not share any homology in structure or amino acid sequence [128] with the other amine oxidases. Non-copper enzymes with similar structures or sequences have not yet been found for any of the three enzymes. 

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