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Protein Science (2004), 13:295-300. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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FOR THE RECORD

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

Preeti Mehta, Krishnamohan Katta and Sankaran Krishnaswamy

Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai-625021, Tamilnadu, India

Reprint requests to: Sankaran Krishnaswamy, School of Biotechnology, Madurai Kamaraj University, Madurai-625021, Tamilnadu, India; e-mail: krishna{at}mrna.tn.nic.in; fax: 91-452-2459105.

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.

Keywords: HNHc domain; hidden Markov models; domain classification; duplication; horizontal transfer; temperate bacteriophages; His-Me endonuclease; McrA


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