The following proteins belongs to a family of proteases which are dependent on the hydrolysis of ATP for their activity and which have a serine in their active site:

• Bacterial ATP-dependent proteases [1,2]. The prototype of those bacterial enzymes is the Escherichia coli La protease (EC 3.4.21.53) (gene lon). La is capable of hydrolyzing large proteins; it degrades short-lived regulatory (such as rcsA and sulA) and abnormal proteins. It is a cytoplasmic protein of 87 Kd that associates as an homotetramer. Its proteolytic activity is stimulated by single-stranded DNA.
• Eukaryotic mitochondrial matrix proteases [3,4]. The prototype of these enzymes is the yeast PIM1 protease. It is a mitochondrial matrix protein of 120 Kd that associated as an homohexamer. It catalyzes the initial step of mitochondrial protein degradation.
• Haemophilus influenzae lon-B (HI1324), a protein which does not contain the ATP-binding domain, but possess a slightly divergent form of the catalytic domain.

The region around the serine residue involved in the catalytic mechanism [5] is perfectly conserved and can be used as a signature pattern.