SODa

SODa predicts whether a protein sequence encodes an Fe/Mn superoxide dismutase and infers its metal specificity, oligomerization state, and candidate residue substitutions to modify these properties.

Key Features:

• Metal Ion Specificity Prediction: Determines whether a sequence uses iron (Fe), manganese (Mn), or is cambialistic (can use either metal).
• Oligomerization Mode Determination: Predicts whether the enzyme adopts a dimeric or tetrameric assembly.
• Residue Substitution Proposals: Suggests specific residue substitutions aimed at changing metal cofactor preference and oligomerization mode.
• Residue and Interaction Fingerprinting: Employs residue fingerprints (conserved residues or residues typical of specific SOD subgroups) and interaction fingerprints (pairs of residues in contact within known SOD structures) as the basis for prediction.

Scientific Applications:

• Oxidative Stress Research: Identifies and characterizes Fe/Mn SODs for studies of cellular oxidative stress defense mechanisms.
• Enzyme Engineering and Rational Protein Design: Provides candidate mutations to tailor metal preference and oligomerization for engineered SOD variants.
• Evolutionary Analysis of Metalloenzymes: Supports analysis of SOD subgroup conservation and metal-utilization patterns across sequences.
• Therapeutic and Industrial Enzyme Development: Aids selection and modification of SODs for potential therapeutic or industrial applications requiring specific metal cofactors or assembly states.

Methodology:

SODa predicts metal specificity, oligomerization, and candidate substitutions using residue fingerprints (conserved or subgroup-typical residues) and interaction fingerprints (pairs of contacting residues derived from known SOD structures).