PDBsum entry: 1qp9

Transcription/DNA

PDB id: 1qp9

Contents

Protein chains

76 a.a. *

71 a.a. *

DNA/RNA

Metals

_ZN ×9

Waters ×96

* Residue conservation analysis

PDB id:

1qp9

Name:

Transcription/DNA

Title:

Structure of hap1-pc7 complexed to the uas of cyc7

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: e, g. Synonym: DNA target of 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').

Source:

Synthetic: yes. Other_details: sequence naturally occuring in yeast. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.80Å R-factor: 0.255 R-free: 0.294

Authors:

A.Lukens,D.King,R.Marmorstein

Key ref:

A.K.Lukens et al. (2000). Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation. Nucleic Acids Res, 28, 3853-3863. PubMed id: 11024163 DOI: 10.1093/nar/28.20.3853

Date:

01-Jun-99 Release date: 09-Oct-00

Protein chains

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

Seq: 1483 a.a.

Struc: 76 a.a.*

Protein chain

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

Seq: 1483 a.a.

Struc: 71 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: sequence-specific DNA binding transcription factor activity (2 terms)

DOI no: 10.1093/nar/28.20.3853

Nucleic Acids Res 28:3853-3863 (2000)

PubMed id: 11024163

Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation.

A.K.Lukens, D.A.King, R.Marmorstein.

ABSTRACT

HAP1 is a transcription factor in yeast whose DNA-binding domain has been implicated in directly affecting transcriptional activation. Two separate mutations in the DNA-binding domain, S63G (HAP1-PC7) and S63R (HAP1-18), retain wild-type binding affinity. However, HAP1-PC7 is transcriptionally silent while HAP1-18 shows highly elevated levels of transcription. We have determined the X-ray crystal structure of the DNA-binding domain of HAP1-PC7 bound to its DNA target, UAS(CYC7), and compared it to the previously solved HAP1-wt and HAP1-18 complexes to UAS(CYC7). Additionally, we have quantitatively compared the DNA-binding affinity and specificity of the HAP1-PC7, HAP1-18 and HAP1-wt DNA-binding domains. We show that, although the DNA-binding domains of these three proteins bind UAS(CYC7) with comparable affinity and specificity, the protein-DNA interactions are dramatically different between the three complexes. Conserved protein-DNA interactions are largely restricted to an internal DNA sequence that excludes one of the two conserved DNA half-sites of UAS(CYC7) suggesting a mode of recognition distinct from other HAP1 family members. Alternative protein-DNA interactions result in divergent DNA configurations between the three complexes. These results suggest that the differential transcriptional activities of the HAP1, HAP1-18 and HAP1-PC7 proteins are due, at least in part, to alternative protein-DNA contacts, and implies that HAP1-DNA interactions have direct allosteric effects on transcriptional activation.