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Biochem J. Apr 15, 1996; 315(Pt 2): 363–367.
PMCID: PMC1217204

A network of specific minor-groove contacts is a common characteristic of paired-domain-DNA interactions.


Pax proteins are a family of transcription factors conserved during evolution and able to bind specific DNA sequences through a domain called a "paired domain'. The DNA-binding specificity of the Pax-8 paired domain was investigated. Site-selection experiments indicate that Pax-8 binds to a consensus sequence similar to those bound by Pax-2 and Pax-5. When consensus sequences of various paired domains are observed in light of recent structural studies describing paired-domain-DNA interaction [Xu, Rould, Jun, Desplan and Pabo (1995) Cell 80, 639-650], it appears that base-pairs contacted in the minor groove are conserved, while most of the base-pairs contacted in the major groove are not. Therefore a network of specific minor groove contacts is a common characteristic of paired-domain-DNA interactions. The functional importance of such a network was successfully tested by analysing the effect of consensus-based mutations on the Pax-8 binding site of the thyroglobulin promoter.

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Selected References

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  • Bopp D, Burri M, Baumgartner S, Frigerio G, Noll M. Conservation of a large protein domain in the segmentation gene paired and in functionally related genes of Drosophila. Cell. 1986 Dec 26;47(6):1033–1040. [PubMed]
  • Burri M, Tromvoukis Y, Bopp D, Frigerio G, Noll M. Conservation of the paired domain in metazoans and its structure in three isolated human genes. EMBO J. 1989 Apr;8(4):1183–1190. [PMC free article] [PubMed]
  • Noll M. Evolution and role of Pax genes. Curr Opin Genet Dev. 1993 Aug;3(4):595–605. [PubMed]
  • Stuart ET, Gruss P. PAX genes: what's new in developmental biology and cancer? Hum Mol Genet. 1995;4(Spec No):1717–1720. [PubMed]
  • Maulbecker CC, Gruss P. The oncogenic potential of Pax genes. EMBO J. 1993 Jun;12(6):2361–2367. [PMC free article] [PubMed]
  • Chalepakis G, Fritsch R, Fickenscher H, Deutsch U, Goulding M, Gruss P. The molecular basis of the undulated/Pax-1 mutation. Cell. 1991 Sep 6;66(5):873–884. [PubMed]
  • Dressler GR, Douglass EC. Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor. Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1179–1183. [PMC free article] [PubMed]
  • Goulding MD, Chalepakis G, Deutsch U, Erselius JR, Gruss P. Pax-3, a novel murine DNA binding protein expressed during early neurogenesis. EMBO J. 1991 May;10(5):1135–1147. [PMC free article] [PubMed]
  • Xu W, Rould MA, Jun S, Desplan C, Pabo CO. Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell. 1995 Feb 24;80(4):639–650. [PubMed]
  • Kozmik Z, Kurzbauer R, Dörfler P, Busslinger M. Alternative splicing of Pax-8 gene transcripts is developmentally regulated and generates isoforms with different transactivation properties. Mol Cell Biol. 1993 Oct;13(10):6024–6035. [PMC free article] [PubMed]
  • Plachov D, Chowdhury K, Walther C, Simon D, Guenet JL, Gruss P. Pax8, a murine paired box gene expressed in the developing excretory system and thyroid gland. Development. 1990 Oct;110(2):643–651. [PubMed]
  • Zannini M, Francis-Lang H, Plachov D, Di Lauro R. Pax-8, a paired domain-containing protein, binds to a sequence overlapping the recognition site of a homeodomain and activates transcription from two thyroid-specific promoters. Mol Cell Biol. 1992 Sep;12(9):4230–4241. [PMC free article] [PubMed]
  • Smith DB, Johnson KS. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene. 1988 Jul 15;67(1):31–40. [PubMed]
  • Kuwabara MD, Sigman DS. Footprinting DNA-protein complexes in situ following gel retardation assays using 1,10-phenanthroline-copper ion: Escherichia coli RNA polymerase-lac promoter complexes. Biochemistry. 1987 Nov 17;26(23):7234–7238. [PubMed]
  • Affolter M, Percival-Smith A, Müller M, Leupin W, Gehring WJ. DNA binding properties of the purified Antennapedia homeodomain. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4093–4097. [PMC free article] [PubMed]
  • Pierrou S, Enerbäck S, Carlsson P. Selection of high-affinity binding sites for sequence-specific, DNA binding proteins from random sequence oligonucleotides. Anal Biochem. 1995 Jul 20;229(1):99–105. [PubMed]
  • Czerny T, Schaffner G, Busslinger M. DNA sequence recognition by Pax proteins: bipartite structure of the paired domain and its binding site. Genes Dev. 1993 Oct;7(10):2048–2061. [PubMed]
  • Czerny T, Busslinger M. DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5). Mol Cell Biol. 1995 May;15(5):2858–2871. [PMC free article] [PubMed]
  • Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. [PMC free article] [PubMed]
  • Chalepakis G, Wijnholds J, Gruss P. Pax-3-DNA interaction: flexibility in the DNA binding and induction of DNA conformational changes by paired domains. Nucleic Acids Res. 1994 Aug 11;22(15):3131–3137. [PMC free article] [PubMed]
  • Spolar RS, Record MT., Jr Coupling of local folding to site-specific binding of proteins to DNA. Science. 1994 Feb 11;263(5148):777–784. [PubMed]
  • Epstein J, Cai J, Glaser T, Jepeal L, Maas R. Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. J Biol Chem. 1994 Mar 18;269(11):8355–8361. [PubMed]
  • Balling R, Deutsch U, Gruss P. undulated, a mutation affecting the development of the mouse skeleton, has a point mutation in the paired box of Pax 1. Cell. 1988 Nov 4;55(3):531–535. [PubMed]
  • Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wüthrich K. Homeodomain-DNA recognition. Cell. 1994 Jul 29;78(2):211–223. [PubMed]
  • Gehring WJ, Affolter M, Bürglin T. Homeodomain proteins. Annu Rev Biochem. 1994;63:487–526. [PubMed]
  • Ekker SC, Jackson DG, von Kessler DP, Sun BI, Young KE, Beachy PA. The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins. EMBO J. 1994 Aug 1;13(15):3551–3560. [PMC free article] [PubMed]
  • Ades SE, Sauer RT. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry. 1995 Nov 7;34(44):14601–14608. [PubMed]
  • Chalepakis G, Gruss P. Identification of DNA recognition sequences for the Pax3 paired domain. Gene. 1995 Sep 11;162(2):267–270. [PubMed]

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