HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily

Protein Sci. 2004 Jan;13(1):295-300. doi: 10.1110/ps.03115604.


The HNHc (SMART ID: SM00507) domain (SCOP nomenclature: HNH family) can be subclassified into at least eight subsets by iterative refinement of HMM profiles. An initial clustering of 323 proteins containing the HNHc domain helped identify the subsets. The subsets could be differentiated on the basis of the pattern of occurrence of seven defining features. Domain association is also different between the subsets. The subsets show organism as well as domain-based clustering, suggestive of propagation by both duplication and horizontal transfer events. Structure-based sequence analysis of the subsets led to the identification of common structural and sequence motifs in the HNH family with the other three families under the His-Me endonuclease superfamily.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / classification
  • Cluster Analysis
  • Conserved Sequence
  • Databases, Protein
  • Endonucleases / chemistry*
  • Endonucleases / classification
  • Endonucleases / genetics
  • Histidine / chemistry*
  • Markov Chains
  • Methionine / chemistry*
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Analysis, Protein
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship


  • Bacterial Proteins
  • Histidine
  • Methionine
  • Endonucleases