1nk2
VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES
Structural highlights
FunctionVND_DROME Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe interactions responsible for the nucleotide sequence-specific binding of the vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding site have been identified. A three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex is presented, with emphasis on the structure of regions of observed protein-DNA contacts. This structure is based on protein-DNA distance restraints derived from NMR data, along with homology modeling, solvated molecular dynamics, and results from methylation and ethylation interference experiments. Helix III of the homeodomain binds in the major groove of the DNA and the N-terminal arm binds in the minor groove, in analogy with other homeodomain-DNA complexes whose structures have been reported. The vnd/NK-2 homeodomain recognizes the unusual DNA consensus sequence 5'-CAAGTG-3'. The roles in sequence specificity and strength of binding of individual amino acid residues that make contact with the DNA are described. We show, based primarily on the observed protein-DNA contacts, that the interaction of Y54 with the DNA is the major determinant of this uncommon nucleotide binding specificity in the vnd/NK-2 homeodomain-DNA complex. Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.,Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA Biochemistry. 1997 May 6;36(18):5372-80. PMID:9154919[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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