Family C42


Summary Holotypes Alignment Tree Genomes Literature

Summary for family C42

Family type peptidaseC42.001 - beet yellows virus-type papain-like peptidase (beet yellows virus), MEROPS Accession MER0002877 (peptidase unit: 502-588)
Content of familyPeptidase family C42 contains polyprotein processing endopeptidases from closteroviruses.
History Identifier created: Handbook of Proteolytic Enzyme, Academic Press, London (1998)
Closteroviruses are plant pathogens that have single-stranded RNA genomes encoding two polyprotein genes, ORF 1a and ORF 1b. The papain-like endopeptidase is located at the N-terminus of the polyprotein derived from ORF 1a. The citrus tristeza virus is exceptional among closteroviruses in that there are two putative papain-like endopeptidases at the N-terminus of the ORF 1a polyprotein: L2 (C42.002) and L1 (C42.003).
Catalytic typeCysteine
Active site residuesC509 H569 
Active siteThe active site consists of a Cys, His catalytic dyad, identified by site-directed mutagenesis in the beet yellows virus (BYV) peptidase (C42.001: Agranovsky et al., 1994).
Activities and specificitiesThe BYV peptidase cleaves a single GlyGly bond, releasing the N-terminal 66 kDa leader protein, which includes the peptidase, from the ORF 1a polyprotein. Proteolysis is believed to occur in cis, but this has not been experimentally confirmed (Agranovsky, 2004). A bulky aliphatic residue occurs in P2 (which is the penultimate residue of the peptidase unit, see the Alignment), a feature that is characteristic of peptidases in clan CA.
Molecular structureThe tertiary structure has not been determined. The leader protein consists of two domains, with the peptidase domain at the C-terminus. The N-terminal domains are not related among the closteroviruses and their functions are unknown.
Basis of clan assignmentActive site residues for members of this family and family C1 occur in the same order in the sequence: C, H.
Distribution of family Bacteria -  
Archaea -  
Protozoa -  
Fungi -  
Plants -  
Animals -  
Viruses details  
Biological functionsThe peptidase releases the N-terminal protein from the polyprotein. Similar activities have been described for other, unrelated viral peptidases including the leader peptidase from the foot-and-mouth disease virus (C28.001) and for togavirin (S03.001). The N-terminal protein has been shown to be important for RNA amplification and cell-to-cell movements of virus particles (Peng et al., 2001, Zinovkin et al., 2003).
ReviewsAgranovsky (2004)
Statistics for family C42Sequences:10
Identifiers with PDB entries:0
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
beet yellows virus-type papain-like peptidaseC42.001-
L2 peptidase (Citrus tristeza virus)C42.002-
L1 peptidase (Citrus tristeza virus)C42.003-
L2 peptidase (grapevine leafroll-associated virus 2)C42.004-
family C42 unassigned peptidasesunassigned-