Talk:Clegg Gal4 sandbox

From Proteopedia

PDB ID 1d66 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
1d66, resolution 2.70Å ()
Ligands:
Structural annotation: Resources: CATH : 1D66B01 InterPro : Ipr007219, Ipr005600, Ipr001138, Ipr002409 Pfam : PF00172, PF03902 SCOP : d1d66a2, d1d66a1, d1d66b1, d1d66b2 UniProt : P04386
Functional annotation: Cellular component: nucleus Biological process: carbohydrate metabolic process positive regulation of transcription by galactose transcription galactose metabolic process regulation of transcription, DNA-dependent Molecular function: transcription factor activity DNA binding metal ion binding transcription activator activity zinc ion binding
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a scene to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, metal binding domain (residues 8-40), an extended linker (41-49), and an alpha-helical dimerization element (50-64). A small, containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

About this Structure

1d66 is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.

See Also

• Gal4
• Hydrogen in macromolecular models
• User:Eric Martz/Introduction to Structural Bioinformatics I
• User:Eric Martz/Introduction to Structural Bioinformatics I%2C 2013
• User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions
• User:Wayne Decatur/Biochem642 Molecular Visualization Sessions

Reference

• Marmorstein R, Carey M, Ptashne M, Harrison SC. DNA recognition by GAL4: structure of a protein-DNA complex. Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122 doi:http://dx.doi.org/10.1038/356408a0