{PDOC51657}
{PS51657; PSRV_HELICASE}
{BEGIN}
*********************************************
* (+)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 alpha- 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 alpha/beta domains (see
<PDB:3VKW>). The    N-terminal  ATP-binding  domain  contains  a parallel six-
stranded beta-sheet  surrounded by four helices on one side and two helices on
the other.  The C-terminal domain contains a parallel four-stranded beta-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: October 2012 / First entry.

[ 1] Gorbalenya A.E., and Koonin E.V. .
     "Helicases: amino acid sequence comparisons and structure-function
     relationships."
     Curr. Opin. Struct. Biol. 3:419-429(1993).
[ 2] Nishikiori M., Sugiyama S., Xiang H., Niiyama M., Ishibashi K.,
     Inoue T., Ishikawa M., Matsumura H., Katoh E.
     "Crystal structure of the superfamily 1 helicase from Tomato mosaic
     virus."
     J. Virol. 86:7565-7576(2012).
     PubMed=22573863; DOI=10.1128/JVI.00118-12
[ 3] Seybert A., van Dinten L.C., Snijder E.J., Ziebuhr J.
     "Biochemical characterization of the equine arteritis virus helicase
     suggests a close functional relationship between arterivirus and
     coronavirus helicases."
     J. Virol. 74:9586-9593(2000).
     PubMed=11000230

--------------------------------------------------------------------------------
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and
distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives
(CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html
--------------------------------------------------------------------------------

{END}