Structure of DNA binding Domain of Human TFAP2A

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors.

Liu, K.Xiao, Y.Gan, L.Li, W.Zhang, J.Min, J.

(2023) Nucleic Acids Res 51: 8270-8282

  • DOI: https://doi.org/10.1093/nar/gkad583
  • Primary Citation of Related Structures:  
    8J0K, 8J0L, 8J0Q, 8J0R

  • PubMed Abstract: 

    The TFAP2 family regulates gene expression during differentiation, development, and organogenesis, and includes five homologs in humans. They all possess a highly conserved DNA binding domain (DBD) followed by a helix-span-helix (HSH) domain. The DBD-HSH tandem domain specifically binds to a GCC(N3)GGC consensus sequence, but the precise recognition mechanisms remain unclear. Here, we found that TFAP2 preferred binding to the GCC(N3)GGC sequence, and the pseudo-palindromic GCC and GGC motifs and the length of the central spacer between the two motifs determined their binding specificity. Structural studies revealed that the two flat amphipathic α-helical HSH domains of TFAP2A stacked with each other to form a dimer via hydrophobic interactions, while the stabilized loops from both DBD domains inserted into two neighboring major grooves of the DNA duplex to form base-specific interactions. This specific DNA binding mechanism controlled the length of the central spacer and determined the DNA sequence specificity of TFAP2. Mutations of the TFAP2 proteins are implicated in various diseases. We illustrated that reduction or disruption of the DNA binding ability of the TFAP2 proteins is the primary cause of TFAP2 mutation-associated diseases. Thus, our findings also offer valuable insights into the pathogenesis of disease-associated mutations in TFAP2 proteins.

  • Organizational Affiliation

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor AP-2-alpha
A, B
219Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05549 (Homo sapiens)
Explore P05549 
Go to UniProtKB:  P05549
PHAROS:  P05549
GTEx:  ENSG00000137203 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05549
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.613α = 90
b = 81.907β = 90
c = 115.939γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770834

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-06
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Refinement description