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PROSITE documentation PDOC51124 [for PROSITE entry PS51124]

Peptidase family C16 domain profile





Description

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]. This domain has a catalytic dyad consisting of a Cys and a downstream His [1,2,4]. 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. 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) [3,5].
  • Human coronavirus (HCoV) 229E papain-like endopeptidase 1 (C16.002) [4].
  • Murine hepatitis coronavirus (MHV) papain-like endopeptidase 1 (PLP1) (C16.001) [6].
  • Porcine epidemic diarrhea virus (PEDV) papain-like endopeptidase 1 (C16.003) [7].
  • Avian infectious bronchitis coronavirus (IBV) papain-like endopeptidase 1 (C16.005) [8].
  • SARS coronavirus papain-like endopeptidase (C16.009) [9].
Last update:

June 2005 / First entry.

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Technical section

PROSITE method (with tools and information) covered by this documentation:

PEPTIDASE_C16, PS51124; Peptidase family C16 domain profile  (MATRIX)


References

1AuthorsZiebuhr J. Snijder E.J. Gorbalenya A.E.
TitleVirus-encoded proteinases and proteolytic processing in the Nidovirales.
SourceJ. Gen. Virol. 81:853-879(2000).
PubMed ID10725411

2AuthorsBaker S.C. Yokomori K. Dong S. Carlisle R. Gorbalenya A.E. Koonin E.V. Lai M.M.C.
TitleIdentification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus.
SourceJ. Virol. 67:6056-6063(1993).
PubMed ID8396668

3AuthorsDong S. Baker S.C.
TitleDeterminants of the p28 cleavage site recognized by the first papain-like cysteine proteinase of murine coronavirus.
SourceVirology 204:541-549(1994).
PubMed ID12805436
DOI10.1128/JVI.77.13.7376-7382.2003

4AuthorsHerold J. Siddell S.G. Gorbalenya A.E.
TitleA human RNA viral cysteine proteinase that depends upon a unique Zn2+-binding finger connecting the two domains of a papain-like fold.
SourceJ. Biol. Chem. 274:14918-14925(1999).
PubMed ID10329692
DOI10.1074/jbc.274.21.14918

5AuthorsKanjanahaluethai A. Jukneliene D. Baker S.C.
TitleIdentification of the murine coronavirus MP1 cleavage site recognized by papain-like proteinase 2.
SourceJ. Virol. 77:7376-7382(2003).
PubMed ID12805436

6AuthorsGosert R. Kanjanahaluethai A. Egger D. Bienz K. Baker S.C.
TitleRNA replication of mouse hepatitis virus takes place at double-membrane vesicles.
SourceJ. Virol. 76:3697-3708(2002).
PubMed ID11907209

7AuthorsKocherhans R. Bridgen A. Ackermann M. Tobler K.
TitleCompletion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence.
SourceVirus Genes 23:137-144(2001).
PubMed ID11724265
DOI10.1023/A:1011831902219

8AuthorsZiebuhr J. Thiel V. Gorbalenya A.E.
TitleThe autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain- like proteases that cleave the same peptide bond.
SourceJ. Biol. Chem. 276:33220-33232(2001).
PubMed ID11431476
DOI10.1074/jbc.M104097200

9AuthorsHarcourt B.H. Jukneliene D. Kanjanahaluethai A. Bechill J. Severson K.M. Smith C.M. Rota P.A. Baker S.C.
TitleIdentification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity.
SourceJ. Virol. 78:13600-13612(2004).
PubMed ID15564471
DOI10.1128/JVI.78.24.13600-13612.2004

E1Titlehttps://www.ebi.ac.uk/merops/cgi-bin/merops.cgi?id=C16;action=summary



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