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Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF - Proteins (2013)

Bottom Line: The enzymes that were experimentally characterized include both narrow-specificity AATases and broad-specificity TATases, as well as AATases with broader-specificity and TATases with narrower-specificity than the previously known family members.Molecular function and phylogenetic analyses underscored the complexity of this family's evolution as the TATase function does not follow a single evolutionary thread, but rather appears independently multiple times during the evolution of the subfamily.The additional functional characterizations described in this article, alongside a detailed sequence and phylogenetic analysis, provide some novel clues to understanding the evolutionary mechanisms at work in this family.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California.

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Venn diagram of conserved residues in AATases and TATases. Those conserved in ≥75% of the sequences for each substrate specificity were identified for the sequence alignment presented in Figure 4, excluding the uncharacterized sequence (AtcAT). Residues in bold type differ from the diagram presented in Rothman and Kirsch.28 Venn.out (written by Daniel Malashock, University of California, Berkeley, not published) was used to perform the sequence analysis to generate this figure.
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fig05: Venn diagram of conserved residues in AATases and TATases. Those conserved in ≥75% of the sequences for each substrate specificity were identified for the sequence alignment presented in Figure 4, excluding the uncharacterized sequence (AtcAT). Residues in bold type differ from the diagram presented in Rothman and Kirsch.28 Venn.out (written by Daniel Malashock, University of California, Berkeley, not published) was used to perform the sequence analysis to generate this figure.

Mentions: The highest percent identity for each row of sequences is in bold, while the lowest is underlined. The enzymes were assigned according to whether they do or do not exhibit high preferences for aspartate compared with aromatic amino acids (see Fig. 5). See text for enzyme name abbreviations.


Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF - Proteins (2013)

Venn diagram of conserved residues in AATases and TATases. Those conserved in ≥75% of the sequences for each substrate specificity were identified for the sequence alignment presented in Figure 4, excluding the uncharacterized sequence (AtcAT). Residues in bold type differ from the diagram presented in Rothman and Kirsch.28 Venn.out (written by Daniel Malashock, University of California, Berkeley, not published) was used to perform the sequence analysis to generate this figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3823064&req=5

fig05: Venn diagram of conserved residues in AATases and TATases. Those conserved in ≥75% of the sequences for each substrate specificity were identified for the sequence alignment presented in Figure 4, excluding the uncharacterized sequence (AtcAT). Residues in bold type differ from the diagram presented in Rothman and Kirsch.28 Venn.out (written by Daniel Malashock, University of California, Berkeley, not published) was used to perform the sequence analysis to generate this figure.
Mentions: The highest percent identity for each row of sequences is in bold, while the lowest is underlined. The enzymes were assigned according to whether they do or do not exhibit high preferences for aspartate compared with aromatic amino acids (see Fig. 5). See text for enzyme name abbreviations.

Bottom Line: The enzymes that were experimentally characterized include both narrow-specificity AATases and broad-specificity TATases, as well as AATases with broader-specificity and TATases with narrower-specificity than the previously known family members.Molecular function and phylogenetic analyses underscored the complexity of this family's evolution as the TATase function does not follow a single evolutionary thread, but rather appears independently multiple times during the evolution of the subfamily.The additional functional characterizations described in this article, alongside a detailed sequence and phylogenetic analysis, provide some novel clues to understanding the evolutionary mechanisms at work in this family.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California.

Show MeSH