PDBsum entry 3cmy

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protein dna_rna ligands links
Transcription regulator/DNA PDB id
Protein chain
60 a.a. *
Waters ×84
* Residue conservation analysis
PDB id:
Name: Transcription regulator/DNA
Title: Structure of a homeodomain in complex with DNA
Structure: Paired box protein pax-3. Chain: a. Fragment: homeodomain (unp residues 219-278). Synonym: hup2. Engineered: yes. 5'-d( Dap Dcp Dap Dtp Dap Dap Dp Dcp Dgp Dap Dtp )-3'. Chain: b. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pax3. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
1.95Å     R-factor:   0.174     R-free:   0.213
Ensemble: 2 models
Authors: G.Birrane,J.A.A.Ladias,A.Soni
Key ref: G.Birrane et al. (2009). Structural basis for DNA recognition by the human PAX3 homeodomain. Biochemistry, 48, 1148-1155. PubMed id: 19199574 DOI: 10.1021/bi802052y
24-Mar-08     Release date:   17-Feb-09    
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Protein chain
Pfam   ArchSchema ?
P23760  (PAX3_HUMAN) -  Paired box protein Pax-3
479 a.a.
60 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1021/bi802052y Biochemistry 48:1148-1155 (2009)
PubMed id: 19199574  
Structural basis for DNA recognition by the human PAX3 homeodomain.
G.Birrane, A.Soni, J.A.Ladias.
The transcription regulatory protein PAX3 binds to cognate DNA sequences through two DNA-binding domains, a paired domain and a homeodomain, and has important functions during neurogenesis and myogenesis. In humans, mutations in the PAX3 gene cause Waardenburg syndrome, whereas a chromosomal translocation that generates a PAX3-FOXO1 fusion gene is associated with the development of alveolar rhabdomyosarcoma. We have determined the crystal structure of the human PAX3 homeodomain in complex with a palindromic DNA containing two inverted TAATC sequences at 1.95 A resolution. Two homeodomains bind to DNA as a symmetric dimer, inducing a 3 degrees bend in the DNA helix. The N-terminal arm of the homeodomain inserts into the minor groove and makes direct and water-mediated interactions with bases and the sugar-phosphate backbone. The recognition helix fits directly into the major groove, and an elaborate network of structurally conserved water molecules mediates the majority of protein-DNA interactions. The structure elucidates the role of serine 50 in selection of the CG sequence immediately 3' of the TAAT motif by PAX class homeodomains and provides insights into the molecular mechanisms by which certain Waardenburg syndrome-associated missense mutations could destabilize the fold of the PAX3 homeodomain whereas others could affect its interaction with DNA.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20127975 V.Pingault, D.Ente, F.Dastot-Le Moal, M.Goossens, S.Marlin, and N.Bondurand (2010).
Review and update of mutations causing Waardenburg syndrome.
  Hum Mutat, 31, 391-406.  
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