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PROSITE documentation PDOC51957

LIM interaction domain (LID) domain profile


LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins are closely related protein families that have roles in determining cell fate, and are required for the correct development of many different organs and tissue types. These proteins all contain a pair of closely spaced LIM domains (see <PDOC00382>) near their N-termini that mediate protein–protein interactions, including binding to the ~30-residue LID (LIM interaction domain) of the Ldb (LIM domain-binding protein) family of ubiquitously expressed cofactors. Ldb is a multi-adaptor protein that mediates interactions between different classes of transcription factors and their co-regulators and the nature of these complexes determines cell fate and differentiation. LID is highly conserved in Ldb proteins across a wide range of species. It can bind the LIM domains of different LMO and LIM-HD proteins (which have sequence identities of as low as 35% within the LIM domains) but not to the LIM domains from other proteins, such as the LIM kinases, which have closely related LIM domains [1,2].

The LID domain forms an extended structure that binds across both LIM domains; it forms short segments of β-strand that augment β-hairpins in the LIM domains (see <PDB:1RUT>). This tandem β-zipper arrangement means that the LID domain forms a number of intermolecular backbone-backbone hydrogen bonds that are additionally stabilized by extensive hydrophobic side chain interactions. Both of these types of interactions do not require strong sequence conservation. Specificity of binding appears to be conferred, at least in part, by a small number of salt-bridges and other hydrogen bonds across the interfaces. A very short hydrophobic-rich stretch of residues that contact LID is highly conserved in the N-terminal LIM domains of the LMO/LIM-HD proteins but not the LIM-kinase proteins [3].

The profile we developed covers the entire LID domain.

Last update:

October 2020 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

LID, PS51957; LIM interaction domain (LID) domain profile  (MATRIX)


1AuthorsMatthews J.M. Bhati M. Craig V.J. Deane J.E. Jeffries C. Lee C. Nancarrow A.L. Ryan D.P. Sunde M.
TitleCompetition between LIM-binding domains.
SourceBiochem. Soc. Trans. 36:1393-1397(2008).
PubMed ID19021562

2AuthorsMatthews J.M. Visvader J.E.
TitleLIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins.
SourceEMBO. Rep. 4:1132-1137(2003).
PubMed ID14647207

3AuthorsDeane J.E. Ryan D.P. Sunde M. Maher M.J. Guss J.M. Visvader J.E. Matthews J.M.
TitleTandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex.
SourceEMBO. J. 23:3589-3598(2004).
PubMed ID15343268

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