PDBsum entry 1ahd

DNA binding protein/DNA

PDB id: 1ahd

Contents

Protein chain

68 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1ahd

Name:

DNA binding protein/DNA

Title:

Determination of the nmr solution structure of an antennapedia homeodomain-DNA complex

Structure:

DNA (5'-d( Gp Ap Ap Ap Gp Cp Cp Ap Tp Tp Ap Gp Ap G)-3'). Chain: a. Engineered: yes. Mutation: yes. DNA (5'-d( Cp Tp Cp Tp Ap Ap Tp Gp Gp Cp Tp Tp Tp C)-3'). Chain: b. Engineered: yes. Homeotic protein antennapedia. Chain: p.

Source:

Synthetic: yes. Drosophila subobscura. Fruit fly. Organism_taxid: 7241. Organ: fruit. Gene: antp. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

16 models

Authors:

M.Billeter,Y.Q.Qian,G.Otting,M.Muller,W.J.Gehring,K.Wuthrich

Key ref:

M.Billeter et al. (1993). Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J Mol Biol, 234, 1084-1093. PubMed id: 7903398

Date:

02-Apr-93 Release date: 31-Oct-93

Protein chain

Q24645  (ANTP_DROSU) -  Homeotic protein antennapedia from Drosophila subobscura

Seq: 394 a.a.

Struc: 68 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-A-A-A-G-C-C-A-T-T-A-G-A-G 14 bases

C-T-C-T-A-A-T-G-G-C-T-T-T-C 14 bases

Enzyme reactions

• Enzyme class: E.C.?

J Mol Biol 234:1084-1093 (1993)

PubMed id: 7903398

Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex.

M.Billeter, Y.Q.Qian, G.Otting, M.Müller, W.Gehring, K.Wüthrich.

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.