{PDOC00382}
{PS00478; LIM_DOMAIN_1}
{PS50023; LIM_DOMAIN_2}
{BEGIN}
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* LIM zinc-binding domain signature and profile *
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Recently [1,2] a number of proteins have  been  found  to  contain a conserved
cysteine-rich domain of about 60 amino-acid residues. These proteins are:

 - Caenorhabditis elegans mec-3; a protein required for the differentiation of
   the set of six touch receptor neurons in this nematode.
 - Caenorhabditis  elegans  lin-11;  a  protein  required  for  the asymmetric
   division of vulval blast cells.
 - Vertebrate insulin gene enhancer binding protein isl-1.  Isl-1 binds to one
   of the two cis-acting protein-binding domains of the insulin gene.
 - Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3.
 - Vertebrate  lmx-1,  which acts as a transcriptional activator by binding to
   the FLAT  element;  a  beta-cell-specific transcriptional enhancer found in
   the insulin gene.
 - Mammalian  LH-2,  a  transcriptional  regulatory  protein  involved  in the
   control of  cell  differentiation  in  developing  lymphoid and neural cell
   types.
 - Drosophila  protein  apterous,  required  for the normal development of the
   wing and halter imaginal discs.
 - Vertebrate protein kinases LIMK-1 and LIMK-2.
 - Mammalian   rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2
   or TTG-2)  are  proteins of about 160 amino acids whose genes are disrupted
   by chromosomal translocations in T-cell leukemia.
 - Mammalian  and  avian cysteine-rich protein (CRP), a 192 amino-acid protein
   of unknown function. Seems to interact with zyxin.
 - Mammalian cysteine-rich intestinal protein (CRIP),  a  small  protein which
   seems to   have   a  role  in  zinc  absorption  and  may  function  as  an
   intracellular zinc transport protein.
 - Vertebrate paxillin, a cytoskeletal focal adhesion protein.
 - Mouse testin. Mouse testin  should not be confused with rat testin which is
   a thiol protease homolog (see <PDOC00126>).
 - Sunflower pollen specific protein SF3.
 - Chicken zyxin. Zyxin is  a low-abundance adhesion plaque protein which  has
   been shown to interact with CRP.
 - Yeast protein LRG1 which is involved in sporulation [4].
 - Yeast rho-type GTPase activating protein RGA1/DBM1.
 - Caenorhabditis elegans homeobox protein ceh-14.
 - Caenorhabditis elegans homeobox protein unc-97.
 - Yeast hypothetical protein YKR090w.
 - Caenorhabditis elegans hypothetical proteins C28H8.6.

These proteins  generally  have two tandem copies of a domain, called LIM (for
Lin-11 Isl-1  Mec-3)  in  their  N-terminal  section.  Zyxin  and paxillin are
exceptions in  that  they  contains respectively three and four LIM domains at
their C-terminal extremity. In apterous, isl-1,  LH-2, lin-11, lim-1 to lim-3,
lmx-1 and  ceh-14  and  mec-3  there  is a homeobox domain some 50 to 95 amino
acids after the LIM domains.

In the  LIM  domain,  there  are  seven  conserved  cysteine  residues  and  a
histidine. The  arrangement followed by these conserved residues is  C-x(2)-C-
x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD]. The   LIM   domain
binds two  zinc  ions  [5].  LIM  does not bind DNA, rather it seems to act as
interface for protein-protein interaction.   We developed a pattern that spans
the first half of the LIM domain.

-Consensus pattern: C-x(2)-C-x(15,21)-[FYWHPCR]-H-x(2)-[CH]-x(2)-C-x(2)-C-
                    x(3)-[LIVMF]
                    [The 5 C's and the H bind zinc]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: 3.

-Last update: April 2005 / Profile revised.

[ 1] Freyd G., Kim S.K., Horvitz H.R.
     "Novel cysteine-rich motif and homeodomain in the product of the
     Caenorhabditis elegans cell lineage gene lin-11."
     Nature 344:876-879(1990).
     PubMed=1970421
[ 2] Baltz R., Evrard J.-L., Domon C., Steinmetz A.
     "A LIM motif is present in a pollen-specific protein."
     Plant Cell 4:1465-1466(1992).
     PubMed=1467648; DOI=10.1105/tpc.4.12.1465
[ 3] Sanchez-Garcia I., Rabbitts T.H.
     Trends Genet. 10:315-320(1994).
[ 4] Mueller A., Xu G., Wells R., Hollenberg C.P., Piepersberg W.
     Nucleic Acids Res. 22:3151-3154(1994).
[ 5] Michelsen J.W., Schmeichel K.L., Beckerle M.C., Winge D.R.
     "The LIM motif defines a specific zinc-binding protein domain."
     Proc. Natl. Acad. Sci. U.S.A. 90:4404-4408(1993).
     PubMed=8506279

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