{PDOC01005}
{PS51295; CRM}
{BEGIN}
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* CRM domain profile *
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The CRM  domain is an ~100-amino acid RNA-binding domain. The name chloroplast
RNA splicing  and  ribosome maturation (CRM) has been suggested to reflect the
functions established  for the four characterized members of the family (CRS1,
CAF1, CAF2  and  YhbY).  The  CRM  domain is found in eubacteria, archaea, and
plants. The  CRM domain is represented as a stand-alone protein in archaea and
bacteria, and  in  single-  and  multidomain  proteins  in plants. It has been
suggested that   prokaryotic   CRM  proteins  existed  as  ribosome-associated
proteins prior  to  the divergence of archaea and bacteria, and that they were
co-opted in  the  plant  lineage  as RNA binding modules by incorporation into
diverse protein  contexts.  Plant CRM domains are predicted to reside not only
in the  chloroplast,  but also in the mitochondrion and the nucleo/cytoplasmic
compartment. The  diversity  of  the  CRM  domain  family in plants suggests a
diverse set of RNA targets [1,2].

The CRM  domain  is  a compact alpha/beta domain consisting of a four-stranded
beta sheet  and  three alpha helices with an alpha-beta-alpha-beta-alpha-beta-
beta topology  (see <PDB:1LN4>). The beta sheet face is basic, consistent with
a role in RNA binding. Proximal to the basic beta sheet face is another moiety
that could contribute to nucleic acid recognition. Connecting strand beta1 and
helix alpha2  is  a  loop  with  a six amino acid motif, GxxG flanked by large
aliphatic residues, within which one 'x' is typically a basic residue [3].

Some proteins known to contain a CRM domain are listed below:

 - Maize  CRS1,  CAF1  and  CAF2 proteins. They contain multiple copies of the
   domain and   are   required  for  the  splicing  of  group  II  introns  in
   chloroplasts.
 - Escherichia coli protein yhbY. It is bound tightly and specifically to pre-
   50S ribosomal subunits, suggesting that it facilitates ribosome maturation.

The profile we developed covers the entire CRM domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Note: The CRM domain has also been called CRS1-YhbY domain [2].

-Last update: February 2007 / Pattern removed, profile added and text revised.

[ 1] Ostheimer G.J., Williams-Carrier R., Belcher S., Osborne E.,
     Gierke J., Barkan A.
     "Group II intron splicing factors derived by diversification of an
     ancient RNA-binding domain."
     EMBO J. 22:3919-3929(2003).
     PubMed=12881426; DOI=10.1093/emboj/cdg372
[ 2] Barkan A., Klipcan L., Ostersetzer O., Kawamura T., Asakura Y.,
     Watkins K.P.
     "The CRM domain: an RNA binding module derived from an ancient
     ribosome-associated protein."
     RNA 13:55-64(2007).
     PubMed=17105995; DOI=10.1261/rna.139607
[ 3] Ostheimer G.J., Barkan A., Matthews B.W.
     "Crystal structure of E. coli YhbY: a representative of a novel class
     of RNA binding proteins."
     Structure 10:1593-1601(2002).
     PubMed=12429100

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