Peptidase family C16 (EC 3.4.22.-) contains the coronaviruses cysteine endopeptidases involved in viral polyprotein processing [E1]. All coronaviruses encodes between one and two accessory cysteine proteinases that recognize and process one or two sites in the amino-terminal half of the replicase polyprotein during assembly of the viral replication complex. MHV, HCoV and TGEV encode two accesssory proteinases, called coronavirus papain-like proteinase 1 and 2 (PL1-PRO and PL2-PRO). IBV and SARS encodes only one called PL-PRO [1]. Coronaviruses papain-like proteinases 1 and 2 have restricted specificities, cleaving respectively two and one bond(s)in the polyprotein. This restricted activity may be due to extended specificity sites: Arg or Lys at the cleavage site position P5 are required for PL1-PRO [2], and Phe at the cleavage site position P6 is required for PL2-PRO [3]. PL1-PRO releases p28 and p65 from the N-terminus of the polyprotein; PL2-PRO cleaves between p210 and p150.

The peptidase family C16 domain is about 260 amino acids in length. This domain is predicted to have an α-β structural organisation known as the papain-like fold. It consists of three α-helices and three strands of antiparallel β-sheet [4]. The active site of the peptidase family C16 domain consists of a catalytic triad of cysteine, histidine, and aspartic acid residues [1,2,4,5,6]. The nucleophilic Cys occurs in the motif Asn-Cys-Xaa-Yaa in which Xaa is an aromatic, hydrophobic residue and Yaa is an aliphatic hydrophobic amino acid. There is little conservation around the general base His. The aspartic acid plays a significant, although not essential role, in orienting and/or stabilizing the substrate in the active site [5]. This peptidase domain also contains Cys residues involved in the formation of a zinc-binding finger which connects the left and right hand domains of a papain-like fold, and may be involved in substrate binding or control the movement of the catalytic domain [4].

Some proteins known to contain a peptidase C16 domain are listed below:

• Murine hepatitis coronavirus (MHV) papain-like endopeptidase 2 (PLP2) (C16.006) [3,7].
• Human coronavirus (HCoV) 229E papain-like endopeptidase 1 (C16.002) [4].
• Murine hepatitis coronavirus (MHV) papain-like endopeptidase 1 (PLP1) (C16.001) [8].
• Porcine epidemic diarrhea virus (PEDV) papain-like endopeptidase 1 (C16.003) [9].
• Avian infectious bronchitis coronavirus (IBV) papain-like endopeptidase 1 (C16.005) [10].
• SARS coronavirus papain-like endopeptidase (C16.009) [11].