PROSITE documentation PDOC00480

Plant viruses icosahedral capsid proteins 'S' region signature

The capsid protein of plant icosahedral positive strand RNA viruses generally consists of four distinct domains: an N-terminal positively charged 'R' domain involved in the interaction with RNA, a connecting arm 'a', a central domain 'S' forming the virion shell, and a C-terminal projecting 'P' domain. Some of the viruses lack either the R or P domains.

It has been shown [1] that the S domain of the capsid protein of a number of plant viruses are evolutionary related, namely:

• Carmoviruses: carnation mottle virus (CarMV), melon necrotic spot virus (MNSV), and turnip crinkle virus (TCV).
• Dianthoviruses: red clover necrotic mosaic virus (RCNMV).
• Sobemoviruses: maize chlorotic mottle virus (MCMV), and southern bean mosaic virus (SBMV).
• Tombusviruses: artichoke mottled crinkle virus (AMCV), cucumber necrosis virus (CNV), cymbidium ringspot virus (CyRSV), and tomato bushy stunt virus (TBSV).
• Tobacco necrosis virus (TNV).

The S domain of these viruses contains from 158 to 166 amino acids and is composed of eight β-strand anti-parallel twisted sheets in what is known as a 'jellyroll' conformation. The signature pattern for this domain starts at the C-terminal part of the 3rd β-strand and extends up to the end of the 4th strand.