maltose binding-a1 homeodomain protein chimera, crystal form II

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.243 

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This is version 1.6 of the entry. See complete history


Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera

Ke, A.Wolberger, C.

(2003) Protein Sci 12: 306-312

  • DOI: https://doi.org/10.1110/ps.0219103
  • Primary Citation of Related Structures:  
    1MH3, 1MH4

  • PubMed Abstract: 

    The Yeast MATa1 and MATalpha2 are homeodomain proteins that bind DNA cooperatively to repress transcription of cell type specific genes. The DNA affinity and specificity of MATa1 in the absence of MATalpha2, however, is very low. MATa1 is converted to a higher affinity DNA-binding protein by its interaction with the C-terminal tail of MATalpha2. To understand why MATa1 binds DNA weakly by itself, and how the MATalpha2 tail affects the affinity of MATa1 for DNA, we determined the crystal structure of a maltose-binding protein (MBP)-a1 chimera whose DNA binding behavior is similar to MATa1. The overall MATa1 conformation in the MBP-a1 structure, which was determined in the absence of alpha2 and DNA, is similar to that in the a1/alpha2/DNA structure. The sole difference is in the C-terminal portion of the DNA recognition helix of MATa1, which is flexible in the present structure. However, these residues are not in a location likely to be affected by binding of the MATalpha2 tail. The results argue against conformational changes in a1 induced by the tail of MATalpha2, suggesting instead that the MATalpha2 tail energetically couples the DNA binding of MATalpha2 and MATa1.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
maltose binding-a1 homeodomain protein chimera421Escherichia coliSaccharomyces cerevisiae
This entity is chimeric
Mutation(s): 3 
Find proteins for P0CY11 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CY11 
Go to UniProtKB:  P0CY11
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0CY11P0AEX9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.254α = 90
b = 88.705β = 90
c = 96.159γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2021-10-27
    Changes: Database references
  • Version 1.6: 2024-02-14
    Changes: Data collection, Refinement description