PDBsum entry 2hdd

Transcription/DNA

PDB id: 2hdd

Contents

Protein chains

55 a.a. *

56 a.a. *

DNA/RNA

Waters ×183

* Residue conservation analysis

PDB id:

2hdd

Name:

Transcription/DNA

Title:

Engrailed homeodomain q50k variant DNA complex

Structure:

DNA (5'- d( Tp Tp Tp Tp Gp Cp Cp Ap Tp Gp Tp Ap Ap Tp Cp Cp C p Cp Gp Gp A)- 3'). Chain: c. Engineered: yes. DNA (5'- d( Ap Tp Cp Cp Gp Gp Gp Gp Ap Tp Tp Ap Cp Ap Tp Gp G p Cp Ap Ap A)- 3'). Chain: d.

Source:

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

Biol. unit:

Tetramer (from PQS)

Resolution:

1.90Å R-factor: 0.205 R-free: 0.251

Authors:

L.Tucker-Kellogg,M.A.Rould,K.A.Chambers,S.E.Ades,R.T.Sauer,C.O.Pabo

Key ref:

L.Tucker-Kellogg et al. (1997). Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. Structure, 5, 1047-1054. PubMed id: 9309220 DOI: 10.1016/S0969-2126(97)00256-6

Date:

10-Feb-98 Release date: 27-May-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.*

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

DNA/RNA chains

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

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

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1016/S0969-2126(97)00256-6

Structure 5:1047-1054 (1997)

PubMed id: 9309220

Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.

L.Tucker-Kellogg, M.A.Rould, K.A.Chambers, S.E.Ades, R.T.Sauer, C.O.Pabo.

ABSTRACT

BACKGROUND: The homeodomain is one of the key DNA-binding motifs used in eukaryotic gene regulation, and homeodomain proteins play critical roles in development. The residue at position 50 of many homeodomains appears to determine the differential DNA-binding specificity, helping to distinguish among binding sites of the form TAATNN. However, the precise role(s) of residue 50 in the differential recognition of alternative sites has not been clear. None of the previously determined structures of homeodomain-DNA complexes has shown evidence for a stable hydrogen bond between residue 50 and a base, and there has been much discussion, based in part on NMR studies, about the potential importance of water-mediated contacts. This study was initiated to help clarify some of these issues. RESULTS: The crystal structure of a complex containing the engrailed Gln50-->Lys variant (QK50) with its optimal binding site TAATCC (versus TAATTA for the wild-type protein) has been determined at 1.9 A resolution. The overall structure of the QK50 variant is very similar to that of the wild-type complex, but the sidechain of Lys50 projects directly into the major groove and makes several hydrogen bonds to the O6 and N7 atoms of the guanines at base pairs 5 and 6. Lys50 also makes an additional water-mediated contact with the guanine at base pair 5 and has an alternative conformation that allows a hydrogen bond with the O4 of the thymine at base pair 4. CONCLUSIONS: The structural context provided by the folding and docking of the engrailed homeodomain allows Lys50 to make remarkably favorable contacts with the guanines at base pairs 5 and 6 of the binding site. Although many different residues occur at position 50 in different homeodomains, and although numerous position 50 variants have been constructed, the most striking examples of altered specificity usually involve introducing or removing a lysine sidechain from position 50. This high-resolution structure also confirms the critical role of Asn51 in homeodomain-DNA recognition and further clarifies the roles of water molecules near residues 50 and 51.

Selected figure(s)

Figure 3.
Figure 3. Major groove contacts of the QK50-TAATCC complex. Three residues make base contacts in the major groove: Asn51 makes a pair of hydrogen bonds with the adenine at bp 3 (red); lle47 makes hydrophobic contacts with the methyl group of the thymine at bp 4 (purple); the primary conformation of Lys50 (yellow) makes hydrogen bonds with the O6 of the guanine at bp 5 and with the O6 and N7 atoms of the guanine at bp 6; the secondary conformation of Lys50 (green) makes hydrogen bonds with the O6 of the guanine at bp 5 and with the O4 of the thymine at bp 4. Hydrogen bonds are shown as dashed lines and van der Waals contacts are indicated with dotted spheres. For clarity, water molecules have been omitted in this figure.

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1047-1054) copyright 1997.

Figure was selected by an automated process.