PDBsum entry 1gd2

Transcription/DNA

PDB id: 1gd2

Contents

Protein chains

65 a.a. *

40 a.a. *

11 a.a. *

DNA/RNA

Waters ×831

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for the diversity of DNA recognition by bzip transcription factors.

Authors

Y.Fujii, T.Shimizu, T.Toda, M.Yanagida, T.Hakoshima.

Ref.

Nat Struct Biol, 2000, 7, 889-893. [DOI no: 10.1038/82822]

PubMed id

11017199

Abstract

The basic region leucine zipper (bZIP) proteins form one of the largest families of transcription factors in eukaryotic cells. Despite relatively high homology between the amino acid sequences of the bZIP motifs, these proteins recognize diverse DNA sequences. Here we report the 2.0 A resolution crystal structure of the bZIP motif of one such transcription factor, PAP1, a fission yeast AP-1-like transcription factor that binds DNA containing the novel consensus sequence TTACGTAA. The structure reveals how the Pap1-specific residues of the bZIP basic region recognize the target sequence and shows that the side chain of the invariant Asn in the bZIP motif adopts an alternative conformation in Pap1. This conformation, which is stabilized by a Pap1-specific residue and its associated water molecule, recognizes a different base in the target sequence from that in other bZIP subfamilies.

Figure 3.
Figure 3. DNA recognition of the Pap1 bZIP motif. a, Stereo view of the basic region of the Pap1 bZIP bound to the major groove of its DNA half site. Hydrogen bonds and van der Waals contacts between protein and DNA are indicated by solid and dotted lines, respectively. b, Diagrams showing protein−DNA interactions in the Pap1−DNA (left) and the GCN4−DNA (right) complexes. Each half site of the DNA is shown. Hydrogen bonds and van der Waals contacts between protein and DNA bases are indicated by solid and dotted black lines, respectively. Interactions with the DNA phosphate backbones are indicated with green lines. c, Schematic representations of DNA recognition by the GCN4 bZIP (left), Pap1 bZIP (middle), and PHO4 bHLH (right) motifs. The conserved amino acid side chains of the motifs that make direct contacts with the DNA bases of the core sequences are shown. Hydrogen bonds are indicated with broken lines and van der Waals contacts with dotted lines. For clarity, water mediated hydrogen bonds are omitted.

Figure 4.
Figure 4. Details of PAP1−DNA interactions. a, Close up view of the hydrophobic interactions (dotted lines) between Phe 93 and the two thymine methyl groups of the TT base pair step. b, Comparison of the side chain conformational changes in the Pap1 and GCN4 bZIP basic regions. The Pap1 side chains (yellow) are superimposed on the GCN4 side chains (green). Hydrogen bonds are indicated by solid lines, with the buried water molecule bridging Gln 90 and the main chain of Asn 86. c, Close up view of the Pap1 bZIP basic region, with the buried water molecule bridging Gln 90 and the main chain of Asn 86. The water molecule also forms hydrogen bonds with the DNA bases. d, Comparison of the side chains of conserved residues of Pap1 (yellow) with the corresponding residues of GCN4 (green).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 889-893) copyright 2000.

Secondary reference #1

Title

Crystallographic characterization of pap1-Dna complex.

Authors

Y.Fujii, T.Ohira, Y.Kyougoku, T.Toda, M.Yanagida, T.Hakoshima.

Ref.

Acta Crystallogr D Biol Crystallogr, 1998, 54, 1014-1016. [DOI no: 10.1107/S0907444998003266]

PubMed id

9757124

Figure 1.
Fig. 1. Crystals of the DNA-binding domain of Pap1 and the cre-13s DNA oligomer. The longest one is 1 mm.

The above figure is reproduced from the cited reference with permission from the IUCr