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1.A.57 The Human SARS Caronavirus Viroporin (SARS-VP) Family

The severe acute respiratory syndrome-associated coronavirus group 26 (SARS CoV) genome includes Orf3a which codes for a protein, Protein 3a (Protein IX; Protein U276; Acessory Protein 3a) of 274 aas that has 3 putative N-terminal TMSs (residues 1-130) and a C-terminal hydrophilic domain (residues 131-274). It is expressed and is found at the surface of SARS-CoV-infected or 3a-cDNA transfected cells (Lu et al, 2006). It forms a homotetrameric (composed of two homodimers) K+-sensitive channel, with intersubunit disulfide bridges. It is inhibited by Ba2+. It appears to be important for release of the virus from the cell but not for replication of the viral DNA (Lu et al, 2006). Protein 3a may be glycosylated (as in the virion) or nonglycosylated.

Accessory protein 3a interacts with several other SARS CoV proteins. These include protein E, protein-7A, the spike M protein and the human small glutamine-rich tetratricopeptide repeat (TPR)-containing protein A [(O43765; 313 aas)].

The SARS CoV envelope small membrane protein E (E protein, sM protein (P59637)) of 76 aas with 1 TMS is the prototype of small homologues (70-90 aas) found in several coronaviruses specific for rats, cats, dogs, mice, people, cows, etc. These include transmissible gastroenteretis virus, mouse hepatitis virus, rat sialodacryoadenitis coronavirus, porcine hemagglutinating encephalomyelitis virus.

The Protein 7A precursor (P59635; protein X4; protein U122; accessory protein 7a) with 122 aas, has 1 TMS and is found in the endoplasmic reticulum/golgi apparatus as well as the virion.

Fourteen ORFs are encoded in the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) genome (Lu et al. 2006). This family of proteins has been referred to as the DUF3092 family. Emodin inhibits current through SARS-associated coronavirus 3a protein (Schwarz et al. 2011). The ion channel activity of the 3a protein is linked to its pro-apoptotic function (Chan et al. 2009).

Protein 3a is a 274 amino acid polytopic channel protein with three putative transmembrane domains (TMDs) encoded by SARS-CoV. Synthetic peptides corresponding to each of its three individual TMSs have been reconstituted into artificial lipid bilayers (Chien et al. 2013). Only TMSs 2 and 3 induced channel activity. Reconstitution of the peptides as TMS1 + TMS3 or TMS2 + TMS3 in a 1: 1 mixture induced membrane activity. In a 1: 1: 1 mixture, channel-like behavior was almost fully restored. Expression of full length 3a and reconstitution into artificial lipid bilayers revealed a weakly cation-selective (PK ≈ 2 PCl ) rectifying channel. In the presence of non-physiological concentrations of Ca2+-ions, channel activity developed.

The sequences of three polytopic viral channel proteins: (i) p7 of HCV and 2B of Polio virus (two TMSs) and (ii) 3a of SARS-CoV (three TMSs were aligned, and the region of overlap was mapped onto structural models of host channels and toxins, focusing on the pore-lining TMSs (Schindler and Fischer 2012). The analysis reveals that p7 and 2B TMSs align with the pore-facing TMS of MscL, and 3a-TMSs align with those of ligand-gated ion channels (Schindler and Fischer 2012). 

The reaction catalyzed by SARS-VP is:

Small molecules (in) small molecules (out)

References associated with 1.A.57 family:

Chan, C.M., H. Tsoi, W.M. Chan, S. Zhai, C.O. Wong, X. Yao, W.Y. Chan, S.K. Tsui, and H.Y. Chan. (2009). The ion channel activity of the SARS-coronavirus 3a protein is linked to its pro-apoptotic function. Int J Biochem. Cell Biol. 41: 2232-2239. 19398035
Chien, T.H., Y.L. Chiang, C.P. Chen, P. Henklein, K. Hänel, I.S. Hwang, D. Willbold, and W.B. Fischer. (2013). Assembling an ion channel: ORF 3a from SARS-CoV. Biopolymers 99: 628-635. 23483519
Lu, W., B.J. Zheng, K. Xu, W. Schwarz, L. Du, C.K. Wong, J. Chen, S. Duan, V. Deubel, and B. Sun. (2006). Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release. Proc. Natl. Acad. Sci. USA 103: 12540-12545. 16894145
Schindler, C. and W.B. Fischer. (2012). Sequence alignment of viral channel proteins with cellular ion channels. J Comput Biol 19: 1060-1072. 22891808
Schwarz, S., K. Wang, W. Yu, B. Sun, and W. Schwarz. (2011). Emodin inhibits current through SARS-associated coronavirus 3a protein. Antiviral Res 90: 64-69. 21356245