Structural and functional significance of the amino acid differences Val(35)Thr, Ser(46)Ala, Asn(65)Ser, and Ala(94)Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV

Three dimensional structures of (chymo)trypsin-like proteinase (3CL(pro)) from SARS-CoV-2 and SARS-CoV differ at 8 positions. We previously found that the Val(86)Leu, Lys(88)Arg, Phe(134)His, and Asn(180)Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CL(pro) relative to each other, which leads to a change in catalytic activity. This conclusion was derived from the comparison of the structural catalytic core in 169 (chymo)trypsin-like proteinases with the serine/cysteine fold. Val(35)Thr, Ser(46)Ala, Asn(65)Ser, Ala(94)Ser mutations were not included in that analysis, since they are located far from the catalytic tetrad. In the present work, the structural and functional roles of these variable amino acids at positions 35, 46, 65, and 94 in the 3CL(pro) sequences of SARS-CoV-2 and SARS-CoV have been established using a comparison of the same set of proteinases leading to the identification of new conservative elements. Comparative analysis showed that, in addition to interdomain mobility, which could modulate catalytic activity, the 3CL(pro)(s) can use for functional regulation an autolytic loop and the unique Asp(33)-Asn(95) region (the Asp(33)-Asn(95) Zone) in the N-terminal domain. Therefore, all 4 analyzed mutation sites are associated with the unique structure-functional features of the 3CL(pro) from SARS-CoV-2 and SARS-CoV. Strictly speaking, the presented structural results are hypothetical, since at present there is not a single experimental work on the identification and characterization of autolysis sites in these proteases.