The Homeodomain Resource: 2003 update

Abstract

The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family. The resource is organized in a compact form and provides user-friendly interfaces for both querying the component databases and assembling customized datasets. The current release (version 5.0, October 2002) contains 1056 full-length homeodomain-containing sequences, 37 experimentally-derived structures, 81 homeodomain interactions, 84 homeodomain DNA-binding sites and 114 homeodomain proteins implicated in human genetic disorders. A new feature of this new release is the inclusion of experimentally-derived protein-protein interaction data for homeodomain family members. All entries are cross-linked for easy retrieval of the original records from source databases. The Homeodomain Resource is freely available through the World Wide Web at http://research.nhgri.nih.gov/homeodomain/.

The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis

“…A set of deuterostome homeodomains downloaded from the Homeodomain Resource [86] were BLASTed against the assembled Nematostella genome. Four kilobase genomic sequences surrounding matches that showed significant similarity to the deuterostome homeodomains (TBLASTN E values < 0.001) were extracted from the genome.…”

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

“…We also exhaustively surveyed the positional conservation of all mouse HD sequences archived in the HD resource and calculated amino acid frequencies at each position (data not shown). 15,27 Residues constituting the hydrophobic core and residues involved in nonspecific (phosphate) as well as specific (base) DNA contacts comprise the most conserved residues, and most of them are also conserved in the mNanHD (Fig. 1d).…”

“…The first, mNanHD K43 , locates to one of the most variable positions within the recognition helix. 27 If an arginine is present, as in 34% of the mouse HD sequences, it likely engages in a phosphate contact as observed, for example, in Ultrabithorax (PDB ID 1b8i) and Antennapedia (PDB ID 9ant). mNanHD K43 might play an analogous role.…”

1H, 13C and 15N chemical shift assignments for the human Pitx2 homeodomain in complex with a 22-base hairpin DNA

“…As one of the four major DNA-binding motifs, the homeodomain is an evolutionarily conserved protein fold that is an integral component of both prokaryotic and eukaryotic transcription factors (Banerjee-Basu et al 2003). It plays important roles in diverse biological processes ranging from embryonic pattern formation to cell-type specification, and differentiation.…”