The cleft between the two domains, the interdomain groove, of endonuclease III in E. coli is a solvent filled pocket lined by polar side chains.  The solvent filled pocket lies between the catalytically important Lys 120 and Asp 138 side chains.  There are seven water molecules in this solvent filled pocket, two water molecules are in an internal cavity and three water molecules are in a shallow depression on the surface opposite the interdomain groove.  Lys 120 is over the mouth of the pocket and could act in a transamination reaction on a damaged base bound in the pocket.  The Lys 120 is a key residue for lyase activity.  The active site of endonuclease III is composed of Lys 120, Asp 138 and Lys 191.  The Lys 120 and Asp 138 are important for catalytic roles whereas Lys 191 plays an important role in DNA binding (11).
 
 

[Introduction][Function][Structure][Reference]

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