PDBsum entry: 1ysa

Transcription/DNA

PDB id: 1ysa

Contents

Protein chains

57 a.a. *

57 a.a. *

DNA/RNA

Waters ×17

* Residue conservation analysis

PDB id:

1ysa

Name:

Transcription/DNA

Title:

The gcn4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex

Structure:

DNA (5'- d( Tp Tp Cp Cp Tp Ap Tp Gp Ap Cp Tp Cp Ap Tp Cp Cp A p Gp Tp T)-3'). Chain: a. Engineered: yes. DNA (5'- d( Ap Ap Ap Cp Tp Gp Gp Ap Tp Gp Ap Gp Tp Cp Ap Tp A p Gp Gp A)-3'). Chain: b.

Source:

Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Biol. unit:

Tetramer (from PQS)

Resolution:

2.90Å R-factor: 0.230

Authors:

T.E.Ellenberger,C.J.Brandl,K.Struhl,S.C.Harrison

Key ref:

T.E.Ellenberger et al. (1992). The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell, 71, 1223-1237. PubMed id: 1473154 DOI: 10.1016/S0092-8674(05)80070-4

Date:

09-Aug-93 Release date: 31-Oct-93

Protein chain

P03069  (GCN4_YEAST) -  General control protein GCN4

Seq: 281 a.a.

Struc: 57 a.a.*

Protein chain

P03069  (GCN4_YEAST) -  General control protein GCN4

Seq: 281 a.a.

Struc: 57 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: nucleic acid binding (4 terms)

DOI no: 10.1016/S0092-8674(05)80070-4

Cell 71:1223-1237 (1992)

PubMed id: 1473154

The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

T.E.Ellenberger, C.J.Brandl, K.Struhl, S.C.Harrison.

ABSTRACT

The yeast transcriptional activator GCN4 is 1 of over 30 identified eukaryotic proteins containing the basic region leucine zipper (bZIP) DNA-binding motif. We have determined the crystal structure of the GCN4 bZIP element complexed with DNA at 2.9 A resolution. The bZIP dimer is a pair of continuous alpha helices that form a parallel coiled coil over their carboxy-terminal 30 residues and gradually diverge toward their amino termini to pass through the major groove of the DNA-binding site. The coiled-coil dimerization interface is oriented almost perpendicular to the DNA axis, giving the complex the appearance of the letter T. There are no kinks or sharp bends in either bZIP monomer. Numerous contacts to DNA bases and phosphate oxygens are made by basic region residues that are conserved in the bZIP protein family. The details of the bZIP dimer interaction with DNA can explain recognition of the AP-1 site by the GCN4 protein.

Selected figure(s)

Figure 4.
Figure 4. Detail of the Frotein-DNA Interactions in the Left Half Site (a) view down the helical axis of the left half site protomer shows the conserved residue, Asn-235, in the center of the protein-DNA interface forming hydrogen onds with 04 of Thy-3 and N4 of Cyt-2'. The basic region a helix is straight n the region of contact with he DNA. Ash-235 is surrounded by the ~ carbons of la-238 and Ala-239, which contact the thymine methyl roups of Thy-3 and Thy-l', respectively. The J~ carbon of Ser-242 also contacts the Thy-3 methyl group. Arg-243, which is conserved in all bZIP proteins (Figure 10), can donate two hydrogen bonds to Gua-0' at the'center of the AP-1 site. Arg-243 of the right half site protomer contacts the phosphates of Cyt-0 and Ade-lL. (b) Schematic of the DNA contacts hown in (a).

Figure 8.
Figure 8. Summary of Protein-DNA Contacts in the GCN4 bZIP Complex (a) Contacts made by the lefthalf site ono- mer. The arrow shows the orientation of the DNA pseudodyad, pointing from the direction of the leucine zipper dimer nterface. (b) Contacts made by the right half mono- mer. This view is related to that in () by rota- tion about the DNA helical axis of approxi- mately 180 °.

The above figures are reprinted by permission from Cell Press: Cell (1992, 71, 1223-1237) copyright 1992.

Figures were selected by the author.