Phylogenetic related proteins

The short-chain alcohol dehydrogenases constitute a second superfamily whose members are widely distributed across all three phylogenetic kingdoms [42,43]. Sequence analysis of the yeast genome revealed a large number of potential proteins that would be part of this superfamily (Table 1), and we have recendy demonstrated that at least one of these is a key player in stereoselective reductions of 3-keto esters (vide infra) and it is likely that closely related proteins may also... 

Although the data on the archaebacterial DNA world are far from exhaustive, it is nevertheless already possible to draw tentative phylogenetic considerations. In their transcription and translation machineries, archaebacteria exhibit several eukaryotic-like features, compared to those in eubacteria, such as an RNA polymerase and elongation factors of the eukaryotic type (see ref. [151], and other chapters of this volume). Several features of the DNA world have been frequently considered to be eukaryotic the presence of histone-like proteins, first HTa[152], more recently HMf[23], the sensitivity of halobacteria to drugs otherwise specific of the eukaryotic DNA topoisomerasell [103], and the existence of an aphidicolin-sensitive DNA polymerase [124]. However, it appears that HTa is a close relative of eubacterial HU proteins (see Fig. 2), that Haloferax Type II DNA topoisomerase is very similar to eubacterial DNA gyrases (see Fig. 9) and that aphidicolin also inhibits an eubacterial DNA polymerase. HMf is clearly homologous to eukaryotic histones, but HMf nucleosomes are drastically different from eukaryotic ones furthermore, one cannot exclude the existence of HMf-related proteins in eubacteria. 

Comparisons of amino acid sequences have revealed that some type 2 copper proteins are phylogenetically related to non-copper proteins of similar func-... 

Galactose oxidase has a unique tertiary structure for a copper protein, comparable with that of the non-copper protein methylamine dehydrogenase. Comparisons of the amino acid sequences [157] show, however, that the enzymes are not phylogenetically related. The tertiary structures developed separately [30]. 

Two phenylalanine hydroxylases have been described, one containing iron and one containing copper. Both are phylogenetically related to the group of enzymes which hydroxylate aromatic amino acids, including tryptophane and tyrosine hydroxylase [187]. No phylogenetic relationship could be constructed to other proteins [183-186,327]. 

All copper proteins which are known to be phylogenetically related to noncopper proteins - i. e., the small blue proteins, metallothioneins and some type 2 copper proteins - are found in single-celled organisms. Hemocyanins, blue oxidases, and those type 2 copper proteins whose functions are essential for multicellular life-forms are not phylogenetically related to non-copper proteins and do not occur in single-celled organisms. 

Balz, M. L. et al. 1982. Phylogenetic aspects of C-reactive protein and related proteins. Annals of the New York Academy of Sciences 389 49-73. 

Figure 1. The phylogenetic relationship among the trypanosomatid deacetylases and other class l/li deacetylases. Related proteins were identified by BLAST analysis. The unrooted neighbour-joining tree was generated using Clustal 1.8X and TreeView. The two classes and the trypanosomatid enzymes (DAC1 -4) are highlighted and all accession numbers are shown. Tb, T. brucei) Tc, T. cruzi Lm, L major, Hs, Homo sapiens Sc, S. cerevisiae Cl, Ciardia lamblia Eh, Entamoeba hiostolytica Pf, Plasmodium falciparum.

Ceruloplasmin a blue, copper-containing glycoprotein, which is present in mammalian blo plasma, and which is phylogenetically related to plant lac-cases and to ascorbate oxidase, both of which are blue. It is a transport and/or storage protein for copper, and it is also an oxidase. Substrates include unsaturated compounds, such as indole derivatives, amphetamine, adrenalin and dopamine. C. has a central role in copper metabolism when C. is absent, as in Wilson s disease, copper is deposited in the tissues, causing death. 

The primary and even tertiary structure of M. and hemoglobins from many different species show striking similarities. M. appears to be phylogenetically the oldest known heme protein, from which hemoglobin evolved as an independent molecule 600 million years ago. M. also appears to be phylogenetically related to Leghemoglobin (see). 

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

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