1A0A

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.

Shimizu, T.Toumoto, A.Ihara, K.Shimizu, M.Kyogoku, Y.Ogawa, N.Oshima, Y.Hakoshima, T.

(1997) EMBO J 16: 4689-4697

  • DOI: 10.1093/emboj/16.15.4689
  • Primary Citation of Related Structures:  
    1A0A

  • PubMed Abstract: 
  • The crystal structure of a DNA-binding domain of PHO4 complexed with DNA at 2.8 A resolution revealed that the domain folds into a basic-helix-loop-helix (bHLH) motif with a long but compact loop that contains a short alpha-helical segment. This helical structure positions a tryptophan residue into an aromatic cluster so as to make the loop compact ...

    The crystal structure of a DNA-binding domain of PHO4 complexed with DNA at 2.8 A resolution revealed that the domain folds into a basic-helix-loop-helix (bHLH) motif with a long but compact loop that contains a short alpha-helical segment. This helical structure positions a tryptophan residue into an aromatic cluster so as to make the loop compact. PHO4 binds to DNA as a homodimer with direct reading of both the core E-box sequence CACGTG and its 3'-flanking bases. The 3'-flanking bases GG are recognized by Arg2 and His5. The residues involved in the E-box recognition are His5, Glu9 and Arg13, as already reported for bHLH/Zip proteins MAX and USF, and are different from those recognized by bHLH proteins MyoD and E47, although PHO4 is a bHLH protein.


    Organizational Affiliation

    Department of Molecular Biology, Nara Institute of Science and Technology, Ikoma, Japan.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)C [auth A], D [auth B]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P07270 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07270 
Go to UniProtKB:  P07270
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3')A [auth C]17N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3')B [auth D]17N/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: 0.284 
      • R-Value Work: 0.230 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 53.51α = 90
      b = 68.3β = 90
      c = 108.77γ = 90
      Software Package:
      Software NamePurpose
      MLPHAREphasing
      X-PLORrefinement
      WEISdata reduction
      CCP4data scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1998-03-18
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance