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Literature DB >> 8557047

Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.

Abstract

even-skipped is a homeobox gene important in controlling segment patterning in the embryonic fruit fly. Its homeobox encodes a DNA binding domain which binds with similar affinities to two DNA consensus sequences, one AT-rich, the other GC-rich. We describe a crystallographic analysis of the Even-skipped homeodomain complexed to an AT-rich oligonucleotide at 2.0 A resolution. The structure reveals a novel arrangement of two homeodomains bound to one 10 bp DNA sequence in a tandem fashion. This arrangement suggests a mechanism for the homeoproteins' regulatory specificity. In addition, the functionally important residue Gln50 is observed in multiple conformations making direct and water-mediated hydrogen bonds with the DNA bases.

Entities: Chemical

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Year: 1995 PMID： 8557047 PMCID： PMC394752 DOI： 10.1002/j.1460-2075.1995.tb00318.x

Source DB: PubMed Journal: EMBO J ISSN： 0261-4189 Impact factor: 11.598

59 in total

1. Differential regulation of transcription preinitiation complex assembly by activator and repressor homeo domain proteins.

Authors: F B Johnson; M A Krasnow
Journal: Genes Dev Date: 1992-11 Impact factor: 11.361

2. Genomes of diploblastic organisms contain homeoboxes: sequence of eveC, an even-skipped homologue from the cnidarian Acropora formosa.

Authors: A Miles; D J Miller
Journal: Proc Biol Sci Date: 1992-05-22 Impact factor: 5.349

3. DNA binding properties of the purified Antennapedia homeodomain.

Authors: M Affolter; A Percival-Smith; M Müller; W Leupin; W J Gehring
Journal: Proc Natl Acad Sci U S A Date: 1990-06 Impact factor: 11.205

4. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.

Authors: J H Ha; R S Spolar; M T Record
Journal: J Mol Biol Date: 1989-10-20 Impact factor: 5.469

5. A single amino acid can determine the DNA binding specificity of homeodomain proteins.

Authors: J Treisman; P Gönczy; M Vashishtha; E Harris; C Desplan
Journal: Cell Date: 1989-11-03 Impact factor: 41.582

6. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain.

Authors: A R Ferré-D'Amaré; G C Prendergast; E B Ziff; S K Burley
Journal: Nature Date: 1993-05-06 Impact factor: 49.962

Review 7. Homeodomain proteins.

Authors: W J Gehring; M Affolter; T Bürglin
Journal: Annu Rev Biochem Date: 1994 Impact factor: 23.643

8. Cooperative binding of an Ultrabithorax homeodomain protein to nearby and distant DNA sites.

Authors: P A Beachy; J Varkey; K E Young; D P von Kessler; B I Sun; S C Ekker
Journal: Mol Cell Biol Date: 1993-11 Impact factor: 4.272

9. Control of neuronal fate by the Drosophila segmentation gene even-skipped.

Authors: C Q Doe; D Smouse; C S Goodman
Journal: Nature Date: 1988-05-26 Impact factor: 49.962

10. The ventral and posterior expression of the zebrafish homeobox gene eve1 is perturbed in dorsalized and mutant embryos.

Authors: J S Joly; C Joly; S Schulte-Merker; H Boulekbache; H Condamine
Journal: Development Date: 1993-12 Impact factor: 6.868

32 in total

1. Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.

Authors: S Sen; L Nilsson
Journal: Biophys J Date: 1999-10 Impact factor: 4.033

2. The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.

Authors: M Schade; C J Turner; R Kühne; P Schmieder; K Lowenhaupt; A Herbert; A Rich; H Oschkinat
Journal: Proc Natl Acad Sci U S A Date: 1999-10-26 Impact factor: 11.205

3. A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos.

Authors: A Carr; M D Biggin
Journal: EMBO J Date: 1999-03-15 Impact factor: 11.598

Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.

1. Differential regulation of transcription preinitiation complex assembly by activator and repressor homeo domain proteins.

2. Genomes of diploblastic organisms contain homeoboxes: sequence of eveC, an even-skipped homologue from the cnidarian Acropora formosa.

3. DNA binding properties of the purified Antennapedia homeodomain.

4. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes.

5. A single amino acid can determine the DNA binding specificity of homeodomain proteins.

6. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain.

Review 7. Homeodomain proteins.

8. Cooperative binding of an Ultrabithorax homeodomain protein to nearby and distant DNA sites.

9. Control of neuronal fate by the Drosophila segmentation gene even-skipped.

10. The ventral and posterior expression of the zebrafish homeobox gene eve1 is perturbed in dorsalized and mutant embryos.

1. Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.

2. The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.

3. A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos.

4. Testing water-mediated DNA recognition by the Hin recombinase.

5. Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.

6. Cysteine 50 of the POU H domain determines the range of targets recognized by POU proteins.

7. Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

8. DNA bending: the prevalence of kinkiness and the virtues of normality.

9. A molecular code dictates sequence-specific DNA recognition by homeodomains.

10. Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.