Summary for clan NA

Summary Alignment Structure Literature
Clan type peptidaseN01.001 - nodavirus peptide lyase (black beetle virus), MEROPS Accession MER0000992 (peptidase unit: 1-407); PDB accession 2BBV
HistoryMEROPS 9.4 (31 January 2011)
DescriptionAsparagine nucleophile; catalytic residues in the order Asp, Asn in sequence; all self-processing endopeptidases
Contents of clanPeptidase clan NA contains autolytic endopeptidases.
EvidenceThe homology of families N1, N2 and N8 is shown by similarities in the protein folds of nodavirus peptidase (N01.001), tetravirus peptidase (N02.001) and poliovirus VP0 protein (N08.001). Also, It has been found that comparison of hidden Markov models for families N1 and N2 by use of the PRC program (http://supfam.mrc-lmb.cam.ac.uk/PRC/) reveals significant similarities (MEROPS: unpublished results).
Catalytic mechanismThe activity of the peptidase is dependent on an Asn at P1, an acidic catalytic residue and destabilization of the scissile bond through local quaternary structure contacts. The acidic side chain of the catalytic residue is buried within a hydrophobic pocket, which ensures that a required hydrogen bond will form between the catalytic residue and the Asn (Reddy et al., 2004).
Peptidase activityThe peptidases in the families are viral capsid proteins. They are thought to autolytically cleave themselves near the C-terminus (families N1 and N2) or N-terminus (family N8) during the late stage of virion assembly. Cleavage in the Picornavirus coat protein VP0 (N08.001) produces proteins VP2 and VP4.
Protein foldTertiary structures have been determined for families N1 (Wery et al., 1994), N2 (Munshi et al., 1998) and N8 (Basavappa et al., 1994). In each case the virion is an icosahedron containing 60 coat proteins arranged in units of three. Each unit is triangular in shape. The coat protein contains two domains, an eight-stranded beta barrel on the surface and a three-helix bundle on the inner face. The active site dyad is part of the helix bundle.
Homologous non-peptidase familiesCoat and capsid proteins from several single-stranded RNA viruses are homologous (Wery et al., 1994), including those from members of the families Comoviridae, Caliciviridae, Bromoviridae, Tymoviridae and Tombusviridae.
Activation mechanismProteolysis occurs only after the subunits of the virion have been assembled. The reaction is very slow with a half life of 4 hours at 26°C.
Other databases PFAMCL0055
SCOP88633

Families

Family Family Type Peptidase Structure
N1 nodavirus peptide lyase (flock house virus) Yes
N2 tetravirus coat protein (Nudaurelia capensis omega virus) Yes
N8 poliovirus capsid VP0-type self-cleaving protein (human poliovirus 1) Yes

Distribution of clan NA among Kingdoms of Organisms

FamilyBacteriaArchaeaProtozoaFungiPlantsAnimalsViruses
N1------+
N2------+
N8+----++
Clan+----++