{PDOC50921}
{PS50921; ANTAR}
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* ANTAR domain profile *
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The ANTAR  (AmiR  and NasR transcription antitermination regulators) domain is
present in  bacterial  regulatory  proteins  that  are  predicted to share the
distinct transcription  antitermination  mechanism reported for amiR and nasR.
Three distinct classes of ANTAR-containing proteins have been identified. Most
proteins are  classical  response  regulators,  where  residues  comprising an
active site are conserved. Therefore, these proteins are predicted to serve as
cognate regulators  for  sensor  histidine  kinases.  Proteins from the second
class are  predicted  to  serve  as  cognate  response  regulators  for sensor
histidine kinases.  Proteins  from  the  second  class are predicted to have a
reponse-regulator fold,   but   lack   residues   that   are   essential   for
phosphotransfer, as  in  amiR.  Finally, some of the ANTAR-containing proteins
are predicted  to  act  as a stand-alone sensory transcriptional regulator. In
addition to the response regulatory domain (see <PDOC50110>), the ANTAR domain
is found associated with GAF, PAC (see <PDOC50112>), STAS (see <PDOC50801>) or
NIT (see <PDOC50906>). The ANTAR domain is supposed to be an RNA-binding motif
[1].

The structure  of  the  ANTAR  domain  has been solved (see <PDB:1QO0; D>) and
shows that  its  C-terminus  is extended into a substantial alpha-helix, which
participates in  a  parallel coiled-coil interaction with the equivalent helix
of the  other  monomer.  The  C-terminus of this helix participates in a three
helix bundle.  The side chains of the most conserved residues of ANTAR domains
are exposed to the cavity formed by the three-helix structure [1,2].

Some proteins known to contain an ANTAR domain are listed below:

 - Pseudomonas  aeruginosa  aliphatic  amidase  regulator  amiR. It acts as an
   antiterminator of  transcription  of  the  amidase operon by preventing the
   formation of a termination stem-loop structure when binding ssRNA.
 - Klebsiella oxytoca nitrate regulatory protein nasR. It binds to the factor-
   independent terminator site located in the nasF operon leader RNA to effect
   transcription antitermination.
 - Azotobacter vinelandii nasT.

The profile we developed spans the entire ANTAR domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: December 2003 / First entry.

[ 1] Shu C.J., Zhulin I.B.
     "ANTAR: an RNA-binding domain in transcription antitermination
     regulatory proteins."
     Trends Biochem. Sci. 27:3-5(2002).
     PubMed=11796212
[ 2] O'Hara B.P., Norman R.A., Wan P.T.C., Roe S.M., Barrett T.E., Drew R.E.,
     Pearl L.H.
     EMBO J. 18:5175-5186(1999).

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