PDBsum entry 3hdd

Transcription/DNA

PDB id: 3hdd

Contents

Protein chains

55 a.a. *

56 a.a. *

DNA/RNA

Waters ×53

* Residue conservation analysis

PDB id:

3hdd

Name:

Transcription/DNA

Title:

Engrailed homeodomain DNA complex

Structure:

5'-d( Tp Tp Tp Tp Gp Cp Cp Ap Tp Gp Tp Ap Ap Tp Tp Ap Cp Cp Tp Ap A)-3'. Chain: c. Fragment: homeodomain. Engineered: yes. 5'-d( Ap Tp Tp Ap Gp Gp Tp Ap Ap Tp Tp Ap Cp Ap Tp Gp Gp Cp Ap Ap A)-3'. Chain: d. Fragment: homeodomain.

Source:

Synthetic: yes. Other_details: homeodomain sequence from drosophila melanogaster (fruit fly). Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Monomer (from PDB file)

Resolution:

2.20Å R-factor: 0.204 R-free: 0.232

Authors:

E.Fraenkel,M.A.Rould,K.A.Chambers,C.O.Pabo

Key ref:

E.Fraenkel et al. (1998). Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. J Mol Biol, 284, 351-361. PubMed id: 9813123 DOI: 10.1006/jmbi.1998.2147

Date:

13-Jul-98 Release date: 11-Nov-98

Protein chain

P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed from Drosophila melanogaster

Seq: 552 a.a.

Struc: 55 a.a.

Protein chain

P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed from Drosophila melanogaster

Seq: 552 a.a.

Struc: 56 a.a.

DNA/RNA chains

T-T-T-T-G-C-C-A-T-G-T-A-A-T-T-A-C-C-T-A-A 21 bases

A-T-T-A-G-G-T-A-A-T-T-A-C-A-T-G-G-C-A-A-A 21 bases

DOI no: 10.1006/jmbi.1998.2147

J Mol Biol 284:351-361 (1998)

PubMed id: 9813123

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures.

E.Fraenkel, M.A.Rould, K.A.Chambers, C.O.Pabo.

ABSTRACT

We report the 2.2 A resolution structure of the Drosophila engrailed homeodomain bound to its optimal DNA site. The original 2.8 A resolution structure of this complex provided the first detailed three-dimensional view of how homeodomains recognize DNA, and has served as the basis for biochemical studies, structural studies and molecular modeling. Our refined structure confirms the principal conclusions of the original structure, but provides important new details about the recognition interface. Biochemical and NMR studies of other homeodomains had led to the notion that Gln50 was an especially important determinant of specificity. However, our refined structure shows that this side-chain makes no direct hydrogen bonds to the DNA. The structure does reveal an extensive network of ordered water molecules which mediate contacts to several bases and phosphates (including contacts from Gln50), and our model provides a basis for detailed comparison with the structure of an engrailed Q50K altered-specificity variant. Comparing our structure with the crystal structure of the free protein confirms that the N and C termini of the homeodomain become ordered upon DNA-binding. However, we also find that several key DNA contact residues in the recognition helix have the same conformation in the free and bound protein, and that several water molecules also are "preorganized" to contact the DNA. Our structure helps provide a more complete basis for the detailed analysis of homeodomain-DNA interactions.

Selected figure(s)

Figure 2.
Figure 2. A, Diagram showing major groove contacts made by wild-type and Q50K engrailed [Tucker-Kellogg et al 1997]. The DNA is represented as a cylindrical projection with phosphates shown as circles; phosphates contacted by the protein are shaded. Contacts from the protein backbone to the DNA are indicated by an oval around the name of the residue. Water molecules in the structure of wild-type engrailed that were also observed in the structure of the free protein are enclosed in boxes. Superimposing the free and bound proteins gives an rms distance. of 0.55 Å for these six water molecules. Those water molecules which surround Ala54 are shaded gray. B, Stereo view of the protein-DNA interface in the wild-type engrailed-DNA complex. DNA is shown in blue with the protein in red. Water molecules are indicated by light blue spheres and hydrogen bonds by broken lines.

Figure 3.
Figure 3. Stereo view showing interactions of the recognition helix in the major groove of engrailed. The backbone of residues 47 to 54 from the recognition helix is shown in red, and base-pairs 3 to 7 are shown in blue. Side-chains of Ile47, Gln50, Asn51 and Ala54 are yellow, with water molecules shown in light blue. Hydrogen bonds are indicated by golden spheres.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 351-361) copyright 1998.

Figures were selected by an automated process.