PDBsum entry 2hos

Transcription/DNA

PDB id: 2hos

Contents

Protein chains

56 a.a. *

58 a.a. *

DNA/RNA

Ligands

GOL ×4

3MO

Waters ×129

* Residue conservation analysis

PDB id:

2hos

Name:

Transcription/DNA

Title:

Phage-selected homeodomain bound to unmodified DNA

Structure:

5'-d( Tp Tp Tp Tp Gp Cp Cp Ap Tp Gp Tp Ap Ap Tp Cp Cp Cp Cp Gp Gp A)-3'. Chain: c. Engineered: yes. 5'-d( Ap Tp Cp Cp Gp Gp Gp Gp Ap Tp Tp Ap Cp Ap Tp Gp Gp Cp Ap Ap A)-3'. Chain: d. Engineered: yes. Segmentation polarity homeobox protein engrailed.

Source:

Synthetic: yes. Other_details: commercial solid phase synthesis. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: en. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.90Å R-factor: 0.225 R-free: 0.257

Authors:

K.M.Shokat,M.E.Feldman,M.D.Simon

Key ref:

M.D.Simon et al. (2006). Structure and properties of a re-engineered homeodomain protein-DNA interface. Acs Chem Biol, 1, 755-760. PubMed id: 17240973 DOI: 10.1021/cb6003756

Date:

16-Jul-06 Release date: 12-Dec-06

Protein chain

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

Seq: 552 a.a.

Struc: 56 a.a.*

Protein chain

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

Seq: 552 a.a.

Struc: 58 a.a.*

* PDB and UniProt seqs differ at 8 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

DOI no: 10.1021/cb6003756

Acs Chem Biol 1:755-760 (2006)

PubMed id: 17240973

Structure and properties of a re-engineered homeodomain protein-DNA interface.

M.D.Simon, M.E.Feldman, D.Rauh, A.E.Maris, D.E.Wemmer, K.M.Shokat.

ABSTRACT

The homeodomain (HD)-DNA interface has been conserved over 500 million years of evolution. Despite this conservation, we have successfully re-engineered the engrailed HD to specifically recognize an unnatural nucleotide using a phage display selection. Here we report the synthesis of novel nucleosides and the selection of mutant HDs that bind these nucleotides using phage display. The high-resolution crystal structure of one mutant in complex with modified and unmodified DNA demonstrates that, even with the substantial perturbation to the interface, this selected mutant retains a canonical HD structure. Dissection of the contributions due to each of the selected mutations reveals that the majority of the modification-specific binding is accomplished by a single mutation (I47G) but that the remaining mutations retune the stability of the HD. These results afford a detailed look at a re-engineered protein-DNA interaction and provide insight into the opportunities for re-engineering highly conserved interfaces.