PDBsum entry 1zq3

Transcription/DNA

PDB id: 1zq3

Contents

Protein chain

68 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1zq3

Name:

Transcription/DNA

Title:

Nmr solution structure of the bicoid homeodomain bound to the consensus DNA binding site taatcc

Structure:

5'-d( Gp Cp Tp Cp Tp Ap Ap Tp Cp Cp Cp Cp G)-3'. Chain: a. Engineered: yes. Other_details: consensus DNA binding site sense strand. 5'-d( Cp Gp Gp Gp Gp Ap Tp Tp Ap Gp Ap Gp C)-3'. Chain: b. Engineered: yes. Other_details: consensus DNA binding site anti-sense strand. Homeotic bicoid protein.

Source:

Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: bcd. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

J.M.Baird-Titus,M.Rance,K.Clark-Baldwin,J.Ma,D.Vrushank

Key ref:

J.M.Baird-Titus et al. (2006). The Solution Structure of the Native K50 Bicoid Homeodomain Bound to the Consensus TAATCC DNA-binding Site. J Mol Biol, 356, 1137-1151. PubMed id: 16406070 DOI: 10.1016/j.jmb.2005.12.007

Date:

18-May-05 Release date: 14-Feb-06

Protein chain

P09081  (BCD_DROME) -  Homeotic protein bicoid from Drosophila melanogaster

Seq: 494 a.a.

Struc: 68 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

G-C-T-C-T-A-A-T-C-C-C-C-G 13 bases

C-G-G-G-G-A-T-T-A-G-A-G-C 13 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2005.12.007

J Mol Biol 356:1137-1151 (2006)

PubMed id: 16406070

The Solution Structure of the Native K50 Bicoid Homeodomain Bound to the Consensus TAATCC DNA-binding Site.

J.M.Baird-Titus, K.Clark-Baldwin, V.Dave, C.A.Caperelli, J.Ma, M.Rance.

ABSTRACT

The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.

Selected figure(s)

Figure 2.
Figure 2. Description of the DNA site used for this study and its structure. (a) Schematic and numbering scheme of the 13mer DNA duplex used for this study. The 5' ends of each strand are base numbers 1 and 14. (b) Three structures of the DNA seen during various stages of the structure calculation. The original B-DNA model created using the program NUCGEN (red), the mean structure after the initial docking calculation (green), and the mean structure after the final energy minimization in the absence of all constraints (blue) are superimposed.

Figure 4.
Figure 4. Superimposed C^a atom ribbon diagrams of 16 homeodomains (see the text for a list). The region of high local RMSD difference between the Bicoid homeodomain (red) and the rest (grey) is labeled with a red arrow. The Bicoid homeodomain contains glycine in position 23, which results in reduced hydrogen-bonding ability to nearby residues and an alteration of the homeodomain structure when compared to the 15 other homeodomain structures. The functional significance of this difference is unknown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 1137-1151) copyright 2006.

Figures were selected by an automated process.