PDBsum entry 2hap

Gene regulation/DNA

PDB id: 2hap

Contents

Protein chains

76 a.a. *

DNA/RNA

Metals

_ZN ×5

Waters ×74

* Residue conservation analysis

PDB id:

2hap

Name:

Gene regulation/DNA

Title:

Structure of a hap1-18/DNA complex reveals that protein/DNA interactions can have direct allosteric effects on transcriptional activation

Structure:

DNA (5'- d( Ap Cp Gp Cp Tp Ap Tp Tp Ap Tp Cp Gp Cp Tp Ap Tp Tp Ap Gp T)-3'). Chain: a. Fragment: upstream activation sequence. Synonym: uas cyc7. Engineered: yes. DNA (5'- d( Ap Cp Tp Ap Ap Tp Ap Gp Cp Gp Ap Tp Ap Ap Tp Ap Gp Cp Gp T)-3'). Chain: b.

Source:

Synthetic: yes. Other_details: sequence from saccharomyces cerevisiae. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: bwg-1-7a-dcyc1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.248 R-free: 0.302

Authors:

D.A.King,L.Zhang,L.Guarente,R.Marmorstein

Key ref:

D.A.King et al. (1999). Structure of HAP1-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation. Nat Struct Biol, 6, 22-27. PubMed id: 9886287 DOI: 10.1038/4893

Date:

17-Sep-98 Release date: 10-Nov-99

Protein chains

P0CS82  (HAP1_YEASX) -  Heme-responsive zinc finger transcription factor HAP1 from Saccharomyces cerevisiae

Seq: 1483 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-C-G-C-T-A-T-T-A-T-C-G-C-T-A-T-T-A-G-T 20 bases

A-C-T-A-A-T-A-G-C-G-A-T-A-A-T-A-G-C-G-T 20 bases

DOI no: 10.1038/4893

Nat Struct Biol 6:22-27 (1999)

PubMed id: 9886287

Structure of HAP1-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation.

D.A.King, L.Zhang, L.Guarente, R.Marmorstein.

ABSTRACT

HAP1 is a yeast transcriptional activator that binds with equal affinity to the dissimilar upstream activation sequences UAS1 and UAS(CYC7), but activates transcription differentially when bound to each site. HAP1-18 harbors an amino acid change in the DNA binding domain. While binding UAS1 poorly, HAP1-18 binds UAS(CYC7) with wild-type properties and activates transcription at elevated levels relative to HAP1. We have determined the structure of HAP1-18-UAS(CYC7) and have compared it to HAP1-UAS(CYC7). Unexpectedly, the single amino acid substitution in HAP1-18 nucleates a significantly altered hydrogen bond interface between the protein and DNA resulting in DNA conformational changes and an ordering of one N-terminal arm of the protein dimer along the DNA minor groove. These observations, together with a large subset of transcriptionally defective mutations in the HAP1 DNA-binding domain that map to the HAP1-DNA interface, suggest that protein-DNA interactions may have direct allosteric effects on transcriptional activation.

Selected figure(s)

Figure 2.
Figure 2. Alignment of HAP1 and HAP1-18 and the protein−DNA interface. a, Allignment of the HAP1 and HAP1-18 DNA complexes showing the entire UAS[CYC7] DNA target and the C trace of the protein dimers. The HAP1 and HAP1-18 complexes are shown in grey and red respectively. The superposition was carried out by aligning the C atoms of each of the protein dimers to one another C r.m.s. deviation is 0.51 Å). The location of the S63R substitution of each protein subunit is shown in blue and the left subunit is numbered according to the discrete domains labeled in Fig. 1. The half sites are highlighted in green. b, Interactions between the left subunit of HAP-18 and UAS[CYC7]. For reference, the DNA target of the HAP1 complex is shown in grey while the DNA of the HAP1-18 complex is shown in red with the DNA half sites highlighted in pink. The left subunit's N-terminal arm, Zn[2]Cys[6] domain and linker are shown as a ribbon with the two zinc atoms shown as yellow balls. Side chains of residues making different interactions as compared to the wild-type protein are shown in green while side chains making conserved interactions in both complexes are shown in yellow. Hydrogen bonds are shown as dashed lines. c, Interactions between the right subunit of HAP1-18 and UAS[ CYC7]. For reference the DNA of both NCS-related molecules of the HAP1 complex are shown in light and dark grey while the DNA of the HAP1-18 complex is shown in red.

Figure 3.
Figure 3. Location of positive control mutations in the HAP1 structure. The two HAP1 subunits are shown in blue and aqua. The DNA is shown in red with the half sites highlighted in green. The most common side chain rotamer of each positive control mutation is modeled onto the HAP1−DNA complex^8 and shown in yellow, and the HAP1-18 mutation is shown in green . Point mutations all evoke the positive control phenotype except PC3, which requires a double mutation at amino acids 98 and 101.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 22-27) copyright 1999.

Figures were selected by an automated process.