1PUF

Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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This is version 1.2 of the entry. See complete history


Literature

STRUCTURE OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA RECOGNITION ANTERIOR TO POSTERIOR

LARONDE-LEBLANC, N.A.Wolberger, C.

(2003) Genes Dev 17: 2060-2072

  • DOI: 10.1101/gad.1103303
  • Primary Citation of Related Structures:  
    1PUF

  • PubMed Abstract: 
  • The HOX/HOM superfamily of homeodomain proteins controls cell fate and segmental embryonic patterning by a mechanism that is conserved in all metazoans. The linear arrangement of the Hox genes on the chromosome correlates with the spatial distribution of HOX protein expression along the anterior-posterior axis of the embryo ...

    The HOX/HOM superfamily of homeodomain proteins controls cell fate and segmental embryonic patterning by a mechanism that is conserved in all metazoans. The linear arrangement of the Hox genes on the chromosome correlates with the spatial distribution of HOX protein expression along the anterior-posterior axis of the embryo. Most HOX proteins bind DNA cooperatively with members of the PBC family of TALE-type homeodomain proteins, which includes human Pbx1. Cooperative DNA binding between HOX and PBC proteins requires a residue N-terminal to the HOX homeodomain termed the hexapeptide, which differs significantly in sequence between anterior- and posterior-regulating HOX proteins. We report here the 1.9-A-resolution structure of a posterior HOX protein, HoxA9, complexed with Pbx1 and DNA, which reveals that the posterior Hox hexapeptide adopts an altered conformation as compared with that seen in previously determined anterior HOX/PBC structures. The additional nonspecific interactions and altered DNA conformation in this structure account for the stronger DNA-binding affinity and altered specificity observed for posterior HOX proteins when compared with anterior HOX proteins. DNA-binding studies of wild-type and mutant HoxA9 and HoxB1 show residues in the N-terminal arm of the homeodomains are critical for proper DNA sequence recognition despite lack of direct contact by these residues to the DNA bases. These results help shed light on the mechanism of transcriptional regulation by HOX proteins and show how DNA-binding proteins may use indirect contacts to determine sequence specificity.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein Hox-A9C [auth A]77Mus musculusMutation(s): 0 
Gene Names: Hoxa9Hox-1.7Hoxa-9
UniProt
Find proteins for P09631 (Mus musculus)
Explore P09631 
Go to UniProtKB:  P09631
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-B-cell leukemia transcription factor-1D [auth B]73Homo sapiensMutation(s): 0 
Gene Names: PBX1PRL
UniProt & NIH Common Fund Data Resources
Find proteins for P40424 (Homo sapiens)
Explore P40424 
Go to UniProtKB:  P40424
PHAROS:  P40424
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP*T)-3'A [auth D]20N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3'B [auth E]20N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      DNA PDBBind:  1PUF Kd: 230 (nM) from 1 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.90 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.233 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 60.769α = 90
      b = 114.853β = 90
      c = 108.17γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing
      CNSrefinement

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2003-09-02
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance