1AHD

DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX

Summary for 1AHD

• Entry DOI: 10.2210/pdb1ahd/pdb
• Descriptor: DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3'), DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), Homeotic protein antennapedia (3 entities in total)
• Functional Keywords: dna binding protein/dna, dna binding protein-dna complex
• Biological source: Drosophila subobscura (Fruit fly)
• Cellular location: Nucleus : Q24645
• Total number of polymer chains: 3
• Total formula weight: 17220.70

Authors

Billeter, M.,Qian, Y.Q.,Otting, G.,Muller, M.,Gehring, W.J.,Wuthrich, K. (deposition date: 1993-04-02, release date: 1993-10-31, Last modification date: 2024-04-10)

Primary citation

Billeter, M.,Qian, Y.Q.,Otting, G.,Muller, M.,Gehring, W.,Wuthrich, K.
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.
J.Mol.Biol., 234:1084-1097, 1993

PubMed Abstract: The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance constraints in the homeodomain, 151 upper distance constraints within the DNA duplex, and 39 intermolecular protein-DNA upper distance constraints. These data were used as the input for the structure calculation with simulated annealing followed by molecular dynamics in a water bath and energy refinement. A group of 16 conformers was thus generated which represent the solution structure of the Antp(C39S) homeodomain-DNA complex. The new structure determination confirms the salient features reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove with the turn of the helix-turn-helix motif outside the contact area with the DNA, and the N-terminal arm of the homeodomain contacting the minor groove of the DNA. In addition, distinct amino acid side-chain-DNA contacts could be identified, and evidence was found that the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium between two or several different DNA contact sites. The molecular dynamics calculations in a water bath yielded structures with hydration water molecules in the protein-DNA interface, which coincides with direct NMR observations of hydration waters. In the Appendix the experimental data obtained with the Antp(C39S) homeodomain-DNA complex and the techniques used for the structure calculation are evaluated using a simulated input data set derived from the X-ray crystal structure of a DNA complex with a homologous homeodomain. This study indicates that a nearly complete set of NOE upper distance constraints for the Antp(C39S) homeodomain and the protein-DNA interface was presently obtained. It further shows that the structure calculation used here yields a precise reproduction of the crystal structure from the simulated input data, and also results in hydration of the protein-DNA interface in the recalculated complex.

PubMed: 7903398
DOI: 10.1006/jmbi.1993.1661

Experimental method

SOLUTION NMR