A SequenceSpace analysis of Lys49 phospholipases A sub(2): clues towards identification of residues involved in a novel mechanism of membrane damage and in myotoxicity

'SequenceSpace' analysis is a novel approach which has been used to identify unique amino acids within a subfamily of phospholipases A sub(2) (PLA sub(2)) in which the highly conserved active site residue Asp49 is substituted by Lys (Lys49-PLA sub(2)s). Although Lys49-PLA sub(2)s do not bind the catalytic co-factor Ca super(2+) and possess extremely low catalytic activity, they demonstrate a Ca super(2+)-independent membrane damaging activity through a poorly understood mechanism, which does not involve lipid hydrolysis. Additionally, Lys49-PLA sub(2)s possess combined myotoxic, oedema forming and cardiotoxic pharmacological activities, however the structural basis of these varied functions is largely unknown. Using the 'SequenceSpace' analysis we have identified nine residues highly unique to the Lys49-PLA sub(2) sub-family, which are grouped in three amino acid clusters in the active site, hydrophobic substrate binding channel and homodimer interface regions. These three highly specific residue clusters may have relevance for the Ca super(2+)-independent membrane damaging activity. Of a further 15 less stringently conserved residues, nine are located in two additional clusters which are well isolated from the active site region. The less strictly conserved clusters have been used in predictive sequence searches to correlate amino acid patterns in other venom PLA sub(2)s with their pharmacological activities, and motifs for presynaptic and combined toxicities are proposed.