{PDOC51005}
{PS51005; NAC}
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* NAC domain profile *
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The NAC  domain (for petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) is an
N-terminal module  of  ~160 amino acids, which is found in proteins of the NAC
family of  plant-specific  transcriptional  regulators  [1].  NAC proteins are
involved in  developmental  processes, including formation of the shoot apical
meristem, floral  organs  and  lateral  shoots,  as  well as in plant hormonal
control and  defence.  The  NAC  domain  is  accompanied by diverse C-terminal
transcriptional activation domains. The NAC domain has been shown to be a DNA-
binding domain (DBD) and a dimerization domain [2,3].

The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is
distinguishable by  blocks of heterogeneous amino acids or gaps. While the NAC
domains were  rich  in  basic  amino  acids  (R,  K  and  H)  as  a whole, the
distribution of  positive  and  negative  amino  acids  in each subdomain were
unequal. Subdomains  C  and D are rich in basic amino acids but poor in acidic
amino acids,  while  subdomain  B  contains  a high proportion of acidic amino
acids. Putative  nuclear  localization  signals  (NLS)  have  been detected in
subdomains C  and  D  [4].  The DBD is contained within a 60 amino acid region
located within subdomains D and E [3]. The overall structure of the NAC domain
monomer consists  of  a  very  twisted  antiparallel  beta-sheet,  which packs
against an  N-terminal  alpha-helix  on  one side and one shorter helix on the
other side  surrounded  by  a  few  helical  elements  (see  <PDB:1UT7>).  The
structure suggests that the NAC domain mediates dimerization through conserved
interactions including  a  salt  bridge, and DNA binding through the NAC dimer
face rich in positive charges [5].

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

 - Petunia NO APICAL MERISTEM (NAM). It acts in the development of embryos and
   flowers.
 - Arabidopsis thaliana CUP-SHAPED COTYLEDON2 (CUC2).
 - Arabidopsis thaliana ATAF1 and ATAF2.
 - Arabidopsis thaliana AtNAM, a transcription factor.
 - Arabidopsis thaliana NAC1. It is involved in root development.
 - Arabidopsis thaliana NAP (NAC-LIKE, ACTIVATED BY AP3/PI).
 - Rice proteins with a NAC domain (OsNACs).
 - Brassica napus proteins with a NAC domain (BnNACs).

The profile we developed covers the entire NAC domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2004 / First entry.

[ 1] Aida M., Ishida T., Fukaki H., Fujisawa H., Tasaka M.
     "Genes involved in organ separation in Arabidopsis: an analysis of the
     cup-shaped cotyledon mutant."
     Plant Cell 9:841-857(1997).
     PubMed=9212461; DOI=10.1105/tpc.9.6.841
[ 2] Xie Q., Frugis G., Colgan D., Chua N.-H.
     "Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to
     promote lateral root development."
     Genes Dev. 14:3024-3036(2000).
     PubMed=11114891
[ 3] Duval M., Hsieh T.-F., Kim S.Y., Thomas T.L.
     "Molecular characterization of AtNAM: a member of the Arabidopsis NAC
     domain superfamily."
     Plant Mol. Biol. 50:237-248(2002).
     PubMed=12175016
[ 4] Kikuchi K., Ueguchi-Tanaka M., Yoshida K.T., Nagato Y., Matsusoka M.,
     "Hirano H.-Y.;
     Molecular analysis of the NAC gene family in rice."
     Mol. Gen. Genet. 262:1047-1051(2000).
     PubMed=10660065;
[ 5] Ernst H.A., Olsen A.N., Skriver K., Larsen S., Lo Leggio L.L.
     "Structure of the conserved domain of ANAC, a member of the NAC family
     of transcription factors."
     EMBO Rep. 5:297-303(2004).
     PubMed=15083810; DOI=10.1038/sj.embor.7400093

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