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PDBsum entry 2hot

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protein dna_rna ligands links
Transcription/DNA PDB id
2hot
Jmol
Contents
Protein chains
56 a.a. *
58 a.a. *
DNA/RNA
Ligands
P2O
GOL ×2
Waters ×80
* Residue conservation analysis
PDB id:
2hot
Name: Transcription/DNA
Title: Phage selected homeodomain bound to modified DNA
Structure: 5'-d( Tp Tp Tp Tp Gp Cp Cp Ap Tp Gp Tp Ap Ap Tp C Gp Gp A)-3'. Chain: c. Engineered: yes. 5'-d( Ap Tp Cp Cp Gp Gp Gp Gp Ap Tp Tp Ap Cp Ap T Ap Ap A)-3'. Chain: d. Engineered: yes. Segmentation polarity homeobox protein engrailed.
Source: Synthetic: yes. Other_details: solid-phase DNA synthesis. Other_details: commercial solid-phase DNA 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:
2.19Å     R-factor:   0.224     R-free:   0.254
Authors: M.E.Feldman,M.D.Simon,K.M.Shokat
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
56 a.a.*
Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
58 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     1 term  

 

 
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.