title: Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
abstract: BACKGROUND
  PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity despite retaining a common core fold and a few critical active site residues. This makes identification of new PD-(D/E)XK nuclease families a challenging task as they usually escape detection with standard sequence-based methods. We developed a modified transitive meta profile search approach and to consider the structural diversity of PD-(D/E)XK nuclease fold more thoroughly we analyzed also lower than threshold Meta-BASIC hits to select potentially correct predictions placed among unreliable or incorrect ones.
  
  
  RESULTS
  Application of a modified transitive Meta-BASIC searches on updated PFAM families and PDB structures resulted in detection of five new PD-(D/E)XK nuclease families encompassing hundreds of so far uncharacterized and poorly annotated proteins. These include four families catalogued in PFAM database as domains of unknown function (DUF506, DUF524, DUF1626 and DUF1703) and YhgA-like family of putative transposases. Three of these families represent extremely distant homologs (DUF506, DUF524, and YhgA-like), while two are newly defined in updated database (DUF1626 and DUF1703). In addition, we also confidently identified an extended AAA-ATPase domain in the N-terminal region of DUF1703 family proteins.
  
  
  CONCLUSIONS
  Obtained results suggest that detailed analysis of below threshold Meta-BASIC hits may push limits further for distant homology detection in the 'midnight zone' of homology. All identified families conserve the core evolutionary fold, secondary structure and hydrophobic patterns common to existing PD-(D/E)XK nucleases and maintain critical active site motifs that contribute to nucleic acid cleavage. Further experimental investigations should address the predicted activity and clarify potential substrates providing further insight into detailed biological role of these newly detected nucleases.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawinskiego 5a, Warsaw, Poland. lukas@icm.edu.pl <lukas@icm.edu.pl>
authors.forename: Lukasz
authors.initials: L
authors.lastname: Knizewski
authors.forename: Lisa N
authors.initials: LN
authors.lastname: Kinch
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
authors.forename: Leszek
authors.initials: L
authors.lastname: Rychlewski
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Ginalski
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment
chemical_list: D015252:Deoxyribonucleases, Type II Site-Specific