A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins

Bioinformatics. 2014 Apr 1;30(7):899-902. doi: 10.1093/bioinformatics/btt661. Epub 2013 Nov 20.


Microtubules are dynamic polymers of tubulin dimers that undergo continuous assembly and disassembly. A mounting number of microtubule-associated proteins (MAPs) regulate the dynamic behavior of microtubules and hence the assembly and disassembly of disparate microtubule structures within the cell. Despite recent advances in identification and functional characterization of MAPs, a substantial number of microtubule accessory factors have not been functionally annotated. Here, using profile-to-profile comparisons and structure modeling, we show that the yeast outer kinetochore components NDC80 and NUF2 share evolutionary ancestry with a novel protein family in mammals comprising, besides NDC80/HEC1 and NUF2, three Intraflagellar Transport (IFT) complex B subunits (IFT81, IFT57, CLUAP1) as well as six proteins with poorly defined function (FAM98A-C, CCDC22, CCDC93 and C14orf166). We show that these proteins consist of a divergent N-terminal calponin homology (CH)-like domain adjoined to an array of C-terminal heptad repeats predicted to form a coiled-coil arrangement. We have named the divergent CH-like domain NN-CH after the founding members NDC80 and NUF2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Calcium-Binding Proteins / chemistry*
  • Calcium-Binding Proteins / genetics
  • Calcium-Binding Proteins / metabolism
  • Evolution, Molecular
  • Humans
  • Kinetochores / metabolism*
  • Microfilament Proteins / chemistry*
  • Microfilament Proteins / genetics
  • Microfilament Proteins / metabolism
  • Molecular Sequence Data
  • Nuclear Proteins / chemistry*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Protein Binding
  • Saccharomyces cerevisiae / chemistry
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Sequence Alignment
  • Sequence Analysis, Protein


  • Calcium-Binding Proteins
  • Microfilament Proteins
  • Nuclear Proteins
  • calponin