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PDBsum entry 1dp7
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Transcription/DNA
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PDB id
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1dp7
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the winged-Helix protein hrfx1 reveals a new mode of DNA binding.
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Authors
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K.S.Gajiwala,
H.Chen,
F.Cornille,
B.P.Roques,
W.Reith,
B.Mach,
S.K.Burley.
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Ref.
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Nature, 2000,
403,
916-921.
[DOI no: ]
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PubMed id
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Abstract
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Regulatory factor X (RFX) proteins are transcriptional activators that recognize
X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any
nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved
76-residue DNA-binding domain (DBD). DNA-binding defects in the protein RFX5
cause bare lymphocyte syndrome or major histocompatibility antigen class II
deficiency. RFX1, -2 and -3 regulate expression of other medically important
gene products (for example, interleukin-5 receptor alpha chain, IL-5R alpha).
Fusions of the ligand-binding domain of the oestrogen receptor with the DBD of
RFX4 occur in some human breast tumours. Here we present a 1.5 A-resolution
structure of two copies of the DBD of human RFX1 (hRFX1) binding cooperatively
to a symmetrical X-box. hRFX1 is an unusual member of the winged-helix subfamily
of helix-turn-helix proteins because it uses a beta-hairpin (or wing) to
recognize DNA instead of the recognition helix typical of helix-turn-helix
proteins. A new model for interactions between linker histones and DNA is
proposed.
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Figure 2.
Figure 2: RFX1 and HNF-3 bold gamma- DBDs.
a, hRFX1 DBD with labelled N and C termini and secondary
structural elements (HTH recognition helix H3, red). b,
Superposition of hRFX1 and HNF-3  DBDs
(r.m.s. deviation for  -carbon
atoms, 3.5 Å), shown in the same orientation as a. c, Stereo
diagram of the hRFX1-DNA 2:1 complex, viewed along the 2-fold
crystallographic symmetry axis relating each half of the
asymmetric unit. Inset, crystallization oligonucleotide, with
blue characters denoting X-box half-sites, labelled A and B. d,
Stereo diagram of HNF-3 bound
to its cognate DNA^6.
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Figure 3.
Figure 3: Protein-DNA interactions. a, Representative 1.5 Å
resolution electron-density map contoured at 2  ,
showing Arg 82 bound to G11 in the major groove of the B
half-site. The crystallization oligonucleotide is inset, with
bold denoting each half-site, and an asterisk identifying the
depicted nucleotide(s). b, Arg 62 bound to G15' in the major
groove of the B halfsite. c, Lys 45 from H3 (red) interacts with
the minor groove face of the A half-site. Red spheres denote
water molecules. d, Direct and water-mediated protein-DNA
contacts made by W1 with the phospho-deoxyribose backbones,
flanking the major groove of the B half-site.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2000,
403,
916-921)
copyright 2000.
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Secondary reference #1
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Title
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Co-Crystal structure of the hnf-3/fork head DNA-Recognition motif resembles histone h5.
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Authors
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K.L.Clark,
E.D.Halay,
E.Lai,
S.K.Burley.
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Ref.
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Nature, 1993,
364,
412-420.
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PubMed id
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Secondary reference #2
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Title
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Crystal structure of globular domain of histone h5 and its implications for nucleosome binding.
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Authors
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V.Ramakrishnan,
J.T.Finch,
V.Graziano,
P.L.Lee,
R.M.Sweet.
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Ref.
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Nature, 1993,
362,
219-223.
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PubMed id
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Secondary reference #3
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Title
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A consensus motif in the rfx DNA binding domain and binding domain mutants with altered specificity.
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Authors
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P.Emery,
M.Strubin,
K.Hofmann,
P.Bucher,
B.Mach,
W.Reith.
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Ref.
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Mol Cell Biol, 1996,
16,
4486-4494.
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PubMed id
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Secondary reference #4
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Title
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Rfx1, A transactivator of hepatitis b virus enhancer i, Belongs to a novel family of homodimeric and heterodimeric DNA-Binding proteins.
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Authors
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W.Reith,
C.Ucla,
E.Barras,
A.Gaud,
B.Durand,
C.Herrero-Sanchez,
M.Kobr,
B.Mach.
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Ref.
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Mol Cell Biol, 1994,
14,
1230-1244.
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PubMed id
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Secondary reference #5
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Title
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Dna binding properties of a chemically synthesized DNA binding domain of hrfx1.
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Authors
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F.Cornille,
P.Emery,
W.Schüler,
C.Lenoir,
B.Mach,
B.P.Roques,
W.Reith.
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Ref.
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Nucleic Acids Res, 1998,
26,
2143-2149.
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PubMed id
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