Supplementary Materials

Supplementary Materials for:

Genomics and evolution of protein phosphatases

Mark J. Chen, Jack E. Dixon, Gerard Manning*

*Corresponding author. Email: manning{at}manninglab.org

This PDF file includes:

  • Text S1. Cataloging the human phosphatome.
  • Text S2. Protein substrates of human protein phosphatases and kinases.
  • Text S3. Cross-references to Entrez Gene models.
  • Text S4. Losses of protein phosphatase subfamilies in humans.
  • Text S5. Human protein phosphatases and disease.
  • Text S6. Structural diversity within the CC1 fold phosphatase domains.
  • Text S7. Human pseudophosphatases and their evolutionary origins.
  • Text S8. PTP family pseudophosphatases.
  • Text S9. Estimating the sizes of the proteomes and kinomes.
  • Fig. S1. Phylogeny of the species used in this study.
  • Fig. S2. Classification of the human phosphatome.
  • Fig. S3. Paladin domain combination and conserved sequence motifs.
  • Fig. S4. Classification of the human protein phosphatome.
  • Fig. S5. Phylogenetic profile of protein phosphatase subfamilies in nine species.
  • Fig. S6. Evolutionary history of protein phosphatases and kinases.
  • Fig. S7. Comparison of the gains and losses of protein phosphatase and kinase subfamilies.
  • Fig. S8. Structure-based sequence alignment of representative CC1 fold phosphatase domains.
  • Fig. S9. The CX5R motif of DSP family pseudophosphatases shows conserved loss of catalytic activity.
  • Fig. S10. The CX5R motif of PTEN family pseudophosphatases.
  • Fig. S11. The CX5R motif of myotubularin family pseudophosphatases, showing conserved loss of catalytic residues.
  • Fig. S12. Loss of the catalytic motif in the TIM50 subfamily.
  • Fig. S13. Comparison of conserved sequence motifs of PPMs.
  • Fig. S14. Comparison of conserved sequence motifs between the PPIP5K subfamily and other HP2 phosphatases.
  • Fig. S15. Predicted PTP pseudophosphatases have alterations to CX5R, KNRY, and WPD motifs.
  • Fig. S16. Substrate overlap of protein phosphatases and kinases at the gene and residue levels.
  • Fig. S17. Workflow for building gene models.
  • Legends for tables S1 to S23
  • Legend for data S1
  • References (84139)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Classification, literature annotation, and published substrate specificity of the human phosphatome.
  • Table S2 (Microsoft Excel format). Substrate preference for each phosphatase fold.
  • Table S3 (Microsoft Excel format). Summary of human phosphatases by family and substrate type.
  • Table S4 (Microsoft Excel format). Catalog of protein phosphatases from nine selected eukaryotes.
  • Table S5 (Microsoft Excel format). Sequence data sets used to build protein phosphatomes.
  • Table S6 (Microsoft Excel format). Subfamily gains and losses of protein phosphatases and kinases.
  • Table S7 (Microsoft Excel format). Protein phosphatase subfamilies expanded in human.
  • Table S8 (Microsoft Excel format). Human protein phosphatase pseudogenes.
  • Table S9 (Microsoft Excel format). Human protein phosphatases and disease.
  • Table S10 (Microsoft Excel format). Human kinases and disease.
  • Table S11 (Microsoft Excel format). Accessory domains in human protein phosphatases.
  • Table S12 (Microsoft Excel format). Domain gains and losses.
  • Table S13 (Microsoft Excel format). Diversity in secondary structure profiles of CC1 fold phosphatase domains.
  • Table S14 (Microsoft Excel format). Secondary structure profile of PTP family phosphatase domain structures.
  • Table S15 (Microsoft Excel format). Secondary structure profile of DSP family phosphatase domain structures.
  • Table S16 (Microsoft Excel format). Secondary structure profile of PTEN family phosphatase domain structures.
  • Table S17 (Microsoft Excel format). Secondary structure profile of myotubularin family phosphatase domain structures.
  • Table S18 (Microsoft Excel format). Secondary structure profiles of the Sac family phosphatase domain structure.
  • Table S19 (Microsoft Excel format). Catalytic motifs by fold.
  • Table S20 (Microsoft Excel format). Catalytically inactive human protein phosphatase domains.
  • Table S21 (Microsoft Excel format). PTP domains known or predicted to lack PTP activity.
  • Table S22 (Microsoft Excel format). Protein substrates of phosphatases and kinases.
  • Table S23 (Microsoft Excel format). Protein phosphatase and kinase subfamilies gained and lost together.
  • Data S1. Sequence alignments and trees of protein phosphatases.

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Citation: M. J. Chen, J. E. Dixon, G. Manning, Genomics and evolution of protein phosphatases. Sci. Signal. 10, eaag1796 (2017).

© 2017 American Association for the Advancement of Science