PDBsum entry 2c6y

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protein dna_rna metals links
Transcription regulation PDB id
Protein chains
98 a.a. *
_MG ×2
Waters ×225
* Residue conservation analysis
PDB id:
Name: Transcription regulation
Title: Crystal structure of interleukin enhancer-binding factor 1 bound to DNA
Structure: Forkhead box protein k2. Chain: a, b. Fragment: DNA-binding domain, residues 251-348. Synonym: interleukin enhancer-binding factor 1, cellular transcription factor ilf-1. Engineered: yes. Interleukin 2 promotor. Chain: c. Other_details: 5'-d( Tp Gp Tp Tp Gp Tp Ap Ap Ap Cp Ap Ap
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Organism_taxid: 9606
Biol. unit: Tetramer (from PDB file)
2.40Å     R-factor:   0.233     R-free:   0.258
Authors: K.-L.Tsai,C.-Y.Huang,C.-H.Chang,Y.-J.Sun,W.-J.Chuang, C.-D.Hsiao
Key ref:
K.L.Tsai et al. (2006). Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins. J Biol Chem, 281, 17400-17409. PubMed id: 16624804 DOI: 10.1074/jbc.M600478200
15-Nov-05     Release date:   18-Apr-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q01167  (FOXK2_HUMAN) -  Forkhead box protein K2
660 a.a.
98 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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


DOI no: 10.1074/jbc.M600478200 J Biol Chem 281:17400-17409 (2006)
PubMed id: 16624804  
Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins.
K.L.Tsai, C.Y.Huang, C.H.Chang, Y.J.Sun, W.J.Chuang, C.D.Hsiao.
Interleukin enhancer binding factor (ILF) is a human transcription factor and a new member of the winged helix/forkhead family. ILF can bind to purine-rich regulatory motifs such as the human T-cell leukemia virus-long terminal region and the interleukin-2 promoter. Here we report the 2.4 A crystal structure of two DNA binding domains of ILF (FOXK1a) binding to a 16-bp DNA duplex containing a promoter sequence. Electrophoretic mobility shift assay studies demonstrate that two ILF-DNA binding domain molecules cooperatively bind to DNA. In addition to the recognition helix recognizing the core sequences through the major groove, the structure shows that wing 1 interacts with the minor groove of DNA, and the H2-H3 loop region makes ionic bonds to the phosphate group, which permits the recognition of DNA. The structure also reveals that the presence of the C-terminal alpha-helix in place of a typical wing 2 in a member of this family alters the orientation of the C-terminal basic residues (RKRRPR) when binding to DNA outside the core sequence. These results provide a new insight into how the DNA binding specificities of winged helix/forkhead proteins may be regulated by their less conserved regions.
  Selected figure(s)  
Figure 3.
Schematic diagram of protein-DNA contacts in the ILF-DBD-DNA (left) and HNF-3γ-DNA complexes (right). Base pairs of the TAAACA sequence are in red boxes. The residues of ILF-DBD1 and ILF-DBD2 that make contact with DNA are colored in black and cyan, respectively. The residues of helix 3 that make contacts with DNA are enclosed within a box. The residues located at the C-terminal region and wing 1 of the DNA binding domain contacting with DNA are highlighted in gray and green boxes, respectively. Hydrogen bonding and van der Waals contacts participating in the base recognition are represented by arrowed thin lines and dotted lines, respectively. Hydrogen bonds and van der Waals contacts to phosphate groups of the DNA backbones are represented by thin lines and dotted lines without arrows, respectively. Water molecules are represented as red balls.
Figure 4.
Stereo views of the recognition helices and DNA interactions. A-C, recognition of the TAAACA core sequence by H3 of ILF-DBD1, ATAACA sequences by H3 of ILF-DBD2, and TCAACC sequence by H3 of HNF-3γ. Hydrogen bonding and van der Waals contacts participating in the base recognition are represented by dashed black lines. Water molecules are represented as green balls. The helix 3 is colored in red in both ILF-DBDs and colored in blue in HNF-3γ.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 17400-17409) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21132356 H.C.Jan, Y.L.Lee, and C.Y.Huang (2011).
Characterization of a Single-Stranded DNA-Binding Protein from Pseudomonas aeruginosa PAO1.
  Protein J, 30, 20-26.  
21416545 Y.P.Chu, C.H.Chang, J.H.Shiu, Y.T.Chang, C.Y.Chen, and W.J.Chuang (2011).
Solution structure and backbone dynamics of the DNA-binding domain of FOXP1: Insight into its domain swapping and DNA binding.
  Protein Sci, 20, 908-924.
PDB code: 2kiu
20615072 Z.Cheng, and M.F.White (2011).
Targeting Forkhead box O1 from the concept to metabolic diseases: lessons from mouse models.
  Antioxid Redox Signal, 14, 649-661.  
20360045 D.R.Littler, M.Alvarez-Fernández, A.Stein, R.G.Hibbert, T.Heidebrecht, P.Aloy, R.H.Medema, and A.Perrakis (2010).
Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence.
  Nucleic Acids Res, 38, 4527-4538.
PDB code: 3g73
20097901 Y.Fujii, and M.Nakamura (2010).
FOXK2 transcription factor is a novel G/T-mismatch DNA binding protein.
  J Biochem, 147, 705-709.  
19274050 S.Hannenhalli, and K.H.Kaestner (2009).
The evolution of Fox genes and their role in development and disease.
  Nat Rev Genet, 10, 233-240.  
18635577 B.A.Benayoun, S.Caburet, A.Dipietromaria, M.Bailly-Bechet, F.Batista, M.Fellous, D.Vaiman, and R.A.Veitia (2008).
The identification and characterization of a FOXL2 response element provides insights into the pathogenesis of mutant alleles.
  Hum Mol Genet, 17, 3118-3127.  
18786403 M.M.Brent, R.Anand, and R.Marmorstein (2008).
Structural basis for DNA recognition by FoxO1 and its regulation by posttranslational modification.
  Structure, 16, 1407-1416.
PDB codes: 3co6 3co7 3coa
18391969 T.Obsil, and V.Obsilova (2008).
Structure/function relationships underlying regulation of FOXO transcription factors.
  Oncogene, 27, 2263-2275.  
17940099 K.L.Tsai, Y.J.Sun, C.Y.Huang, J.Y.Yang, M.C.Hung, and C.D.Hsiao (2007).
Crystal structure of the human FOXO3a-DBD/DNA complex suggests the effects of post-translational modification.
  Nucleic Acids Res, 35, 6984-6994.
PDB code: 2uzk
17189638 L.A.Cirillo, and K.S.Zaret (2007).
Specific interactions of the wing domains of FOXA1 transcription factor with DNA.
  J Mol Biol, 366, 720-724.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.