Bioinformatic analysis of guanylyl/adenylyl cyclases family
This example is discussed in detail in Suplatov (2014) J Biomol Struct Dyn

Bioinformatic analysis of a family of homologous guanylyl and adenylyl cyclases (GCs and ACs respectively) has been performed to reveal subfamily-specific positions responsible for nucleotide discrimination. GCs and ACs play fundamental roles in upregulation of kinases and modulation of ion channels in a wide range of cellular processes. While guanylyl cyclases use GTP as a substrate to form cGMP, adenylyl cyclases catalyze the stereochemically analogous conversion of ATP to cAMP (Eckstein, 1981; Gerlt, 1980).

A set of 23 most statistically significant SSPs was identified (Table 1). Positions 1005D/C and 938K/E from the active site area are the most high-scoring hits in the family and seem to be especially important. Indeed, mutations 1005C→D and 938E→K were previously experimentally confirmed to completely alter the nucleotide specificity of guanylyl cyclase from GTP to ATP (Tucker, 1998). Thus, subfamily-specific positions responsible for nucleotide discrimination were automatically identified with only publicly available sequence and structural information without pre-defined functional classification.

Input data (Manual mode)

  • Multiple sequence alignment file
  • Gap threshold: 30 (%)
  • Reference sequence: 1 (first sequence from the alignment file)
  • Offset: 874
  • Number of random permutations: 1000
  • Coordinate PDB file
  • Active site definition: ATP 10 (10Å around crystallographic ATP molecule)
  • 3D-mode: 4Å, 1000 random permutations to calculate conserved positions
  • Outliers: 0.2 (not more than 20% from the samle size)
  • Subfamily size limit: 3 sequences

Output data: download

Table 1. Subfamily-specific positions in guanylyl/adenylyl cyclases

Top 10 positions are shown. Hits are ranked in declined statistical significance. Positions are numbered as in C2 catalytic region of type II rat adenylyl cyclase PDB 1AB8. Most frequently occurring residues are shown for every subfamily. * catalytic site residues.