1QP9

STRUCTURE OF HAP1-PC7 COMPLEXED TO THE UAS OF CYC7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

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This is version 1.3 of the entry. See complete history


Literature

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

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

(2000) Nucleic Acids Res 28: 3853-3863

  • DOI: 10.1093/nar/28.20.3853
  • Primary Citation of Related Structures:  
    1QP9

  • PubMed 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 ...

    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.


    Related Citations: 
    • Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein
      King, D., Zhang, L., Guarente, L., Marmorstein, R.
      (1999) Nat Struct Biol 6: 64
    • Structure of HAP-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation
      King, D., Zhang, L., Guarente, L., Marmorstein, R.
      (1999) Nat Struct Biol 6: 22
    • Asymmetric binding and transactivation properties of the HAP1 DNA binding domain
      King, D.
      (1999) Thesis --: --

    Organizational Affiliation

    The Wistar Institute and The Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYP1(HAP1-PC7) ACTIVATORY PROTEINE [auth A],
F [auth B],
G [auth C],
H [auth D]
76Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: HAP1CYP1
UniProt
Find proteins for P0CS82 (Saccharomyces cerevisiae)
Explore P0CS82 
Go to UniProtKB:  P0CS82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CS82
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')A [auth E],
C [auth G]
20N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')B [auth F],
D [auth H]
20N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.9α = 90
b = 90.9β = 90
c = 96.5γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations