Replicase Polyprotein 1ab (Rep) (orf1ab) Human SARS Coronavirus Recombinant Protein

Function: The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products

By similarity. Ref.30 Ref.31 Ref.32The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3. Ref.30 Ref.31 Ref.32The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK

By similarity. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function. Ref.30 Ref.31 Ref.32The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G). Activity of helicase is dependent on magnesium. Ref.30 Ref.31 Ref.32The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction. Ref.30 Ref.31 Ref.32Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter. Ref.30 Ref.31 Ref.32Nsp9 is a ssRNA-binding protein. Ref.30 Ref.31 Ref.32NendoU is a Mn2+-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond. Ref.30 Ref.31 Ref.32

Catalytic activity: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Ref.25ATP + H2O = ADP + phosphate. Ref.25TSAVLQ-|-SGFRK-NH2 and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position. Ref.25Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). Ref.25

Subunit structure: 3CL-PRO exists as monomer and homodimer. Only the homodimer shows catalytic activity. Eight copies of nsp7 and eight copies of nsp8 assemble to form a heterohexadecamer. Nsp9 is a dimer. Nsp10 forms a dodecamer

By similarity. Interacts (via N-terminus) with DDX1. Ref.25 Ref.33 Ref.38

Subcellular location: Non-structural protein 3: Host membrane; Multi-pass membrane protein

Potential. Non-structural protein 4: Host membrane; Multi-pass membrane protein

Potential. Non-structural protein 6: Host membrane; Multi-pass membrane protein

Potential. Non-structural protein 7: Host cytoplasm › host perinuclear region

By similarity. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes

By similarity.Non-structural protein 8: Host cytoplasm › host perinuclear region

By similarity. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes

By similarity.Non-structural protein 9: Host cytoplasm › host perinuclear region

By similarity. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes

By similarity.Non-structural protein 10: Host cytoplasm › host perinuclear region

By similarity. Note: nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes

By similarity.Helicase: Host endoplasmic reticulum-Golgi intermediate compartment

Potential. Note: The helicase interacts with the N protein in membranous complexes and colocalizes with sites of synthesis of new viral RNA

By similarity.Uridylate-specific endoribonuclease: Host cytoplasm › host perinuclear region

By similarity.

Domain: The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane. Ref.25

Post-translational modification: Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed

By similarity.

Sequence similarities: Belongs to the coronaviruses polyprotein 1ab family.Contains 1 (+)RNA virus helicase ATP-binding domain.Contains 1 (+)RNA virus helicase C-terminal domain.Contains 1 CV MBD (coronavirus metal-binding) domain.Contains 1 Macro domain.Contains 1 peptidase C16 domain.Contains 1 peptidase C30 domain.Contains 1 RdRp catalytic domain.

Caution: Isolates SZ3 and SZ16 have been isolated from Paguma larvata and are described as SARS-like in litterature.

Biophysicochemical propertiesKinetic parameters:The kinetic parameters are studied for the 3C-like proteinase domain. The cleavage takes place at the /.KM=1.15 mM for peptide TSAVLQ/SGFRK-NH2 Ref.25KM=0.58 mM for peptide SGVTFQ/GKFKKKM=1.44 mM for peptide ATVRLQ/AGNATpH dependence:Optimum pH is 7.0 for 3C-like proteinase activity.

Sequence caution: The sequence AAP13440.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAP41036.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAP82975.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAP97881.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAQ01596.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAQ01608.1 differs from that shown. Reason: Erroneous gene model prediction.