PROSITE documentation PDOC51657
(+)RNA virus helicase core domain profile


Helicases have been classified in 6 superfamilies (SF1-SF6) [1,2]. All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) (see <PDOC00017>) and Walker B (Mg2+-binding aspartic acid) motifs [1]. The two largest superfamilies, commonly referred to as SF1 and SF2 (see <PDOC51192>), share similar patterns of seven conserved sequence motifs, some of which are separated by long poorly conserved spacers [1]. Helicase motifs appear to be organized in a core domain which provides the catalytic function, whereas optional inserts and amino- and carboxy-terminal sequences may comprise distinct domains with diverse accessory roles. The helicase core contains two structural domains, an N-terminal ATP-binding domain and a C-terminal domain. Putative SF1 helicases are extremely widespread among positive-stranded (+)RNA viruses. They have been identified in a variety of plant virus families, as well as α- rubi-, arteri-, hepatitis E, and coronaviruses. A number of these viral enzymes have been implicated in diverse aspects of transcription and replication but also in RNA stability and cell-to-cell movement [3].

The (+)RNA virus helicase core contains two RecA-like α/β domains (see <PDB:3VKW>). The N-terminal ATP-binding domain contains a parallel six-stranded β-sheet surrounded by four helices on one side and two helices on the other. The C-terminal domain contains a parallel four-stranded β-sheet sandwiched between two helices on each of its sides. The (+)RNA virus helicase core is likely to bind NTP in cleft between the N-terminus of the ATP-binding domain and the beginning of the C-terminal domain [2].

The profile we developed covers the entire (+)RNA virus helicase core.

Last update:

October 2012 / First entry.


Technical section

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

PSRV_HELICASE, PS51657; (+)RNA virus helicase core domain profile  (MATRIX)


1AuthorsGorbalenya A.E. and Koonin E.V. .
TitleHelicases: amino acid sequence comparisons and structure-function relationships.
SourceCurr. Opin. Struct. Biol. 3:419-429(1993).

2AuthorsNishikiori M. Sugiyama S. Xiang H. Niiyama M. Ishibashi K. Inoue T. Ishikawa M. Matsumura H. Katoh E.
TitleCrystal structure of the superfamily 1 helicase from Tomato mosaic virus.
SourceJ. Virol. 86:7565-7576(2012).
PubMed ID22573863

3AuthorsSeybert A. van Dinten L.C. Snijder E.J. Ziebuhr J.
TitleBiochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicases.
SourceJ. Virol. 74:9586-9593(2000).
PubMed ID11000230

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