1NK2

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES

1NK2 の概要

• エントリーDOI: 10.2210/pdb1nk2/pdb
• NMR情報: BMRB: 4141
• 分子名称: DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3'), DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3'), HOMEOBOX PROTEIN VND (3 entities in total)
• 機能のキーワード: homeodomain, homeobox, dna-binding protein, embryonic development, complex (homeodomain-dna), dna binding protein-dna complex, dna binding protein/dna
• 由来する生物種: Drosophila melanogaster (fruit fly)
• 細胞内の位置: Nucleus (Probable): P22808
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 19171.12

構造登録者

Gruschus, J.M.,Tsao, D.H.H.,Wang, L.-H.,Nirenberg, M.,Ferretti, J.A. (登録日: 1998-05-06, 公開日: 1999-02-23, 最終更新日: 2024-05-22)

主引用文献

Gruschus, J.M.,Tsao, D.H.,Wang, L.H.,Nirenberg, M.,Ferretti, J.A.
Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
Biochemistry, 36:5372-5380, 1997

PubMed Abstract: The 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.

PubMed: 9154919
DOI: 10.1021/bi9620060

実験手法

SOLUTION NMR