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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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nucleus
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2 terms
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Biological process
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multicellular organismal development
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21 terms
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Biochemical function
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transcription regulatory region DNA binding
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8 terms
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DOI no:
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J Mol Biol
289:683-690
(1999)
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PubMed id:
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Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex.
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C.Jin,
I.Marsden,
X.Chen,
X.Liao.
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ABSTRACT
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Genesis is an HNF-3/fkh homologous protein. By using multi-dimensional NMR
techniques, we have obtained the solution structure and backbone dynamics of
Genesis complexed with a 17 base-pair DNA. Our results indicate that both the
local folding and dynamic properties of Genesis are perturbed when it binds to
the DNA site. Our data show that a conserved flexible amino acid sequence (wing
1) makes dynamic contacts to DNA in the complex and a short helix is induced by
Genesis-DNA interactions. Our data indicate that, unlike the HNF-3gamma/DNA
complex, a magnesium ion is not required in forming the stable Genesis-DNA
complex.
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Selected figure(s)
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Figure 2.
Figure 2. The structure of the Genesis-DNA complex (access number 2HDC). (a) Summary of the backbone NOE
evidence for the secondary structure of Genesis in the DNA complex. E101 and L102 are fused amino acid residues
to generate a XhoI restriction site in expression vector pET21. (b) A stereo diagram showing the superposition of the
20 best calculated DYANA structures of the Genesis-DNA complex. Only amino acid residues V2 to K98 are shown.
A total of 200 structures were calculated using 40,000 steps in energy minimization: 201 short-range, 619 medium-
range, and 227 long-range (total 1047) NOE restraints in the protein and 79 restraints between the protein and DNA
were used for the structure calculation; 29 pseudo linkers were used between the protein and DNA, and 27 linkers
were used between the two strands of DNA. The DNA conformation is assumed to be B-form by using constraints
measured from an ideal B-type DNA. The distance between two atoms of the DNA is refined to the ideal distance in
the B-form DNA by an upper limit and a lower limit constraint pair (dupper
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dlower
=
0.45 Å ): 1720 constraint pairs
for the DNA are used in the DYANA calculation. The constraint violation analysis was performed with DYANA
program. From 0.2 to 0.3 Å , 218 violations are detected; 0.3
~
0.4 Å , 64 constraint violations are observed;
0.4
~
0.5 Å , 13 violations are observed; and 0.5
~
0.6 Å , 3 violations are detected. In all, 135, 51, and 112 constraints
are violated within the protein, between the protein and DNA, and within DNA, respectively. Therefore, the average
violation is 17.3 per structure between 0.2 and
~0.6
Å . The results of a Ramachandran analysis for non-glycine and
non-proline residues (2-98) are 70.6 % in the most favored regions, 21.4 % in additional allowed regions, 7.2 % in gen-
erously allowed regions, and 0.8 % in disallowed regions. (c) The DNA sequence used to form the complex and the
proposed DNA contacts in the DNA core sequence important for Genesis recognition. (S) Sense strand of DNA;
(A) antisense strand of DNA.
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Figure 3.
Figure 3. A ribbon diagram showing the NMR-
derived tertiary structure of the Genesis-DNA complex.
The structure was analyzed and produced with the
program MOLMOL (Koradi et. al., 1996).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
289,
683-690)
copyright 1999.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Lin,
T.Zhou,
and
J.Wang
(2011).
Solution structure of the human HSPC280 protein.
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Protein Sci, 20,
216-223.
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PDB code:
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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.
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Protein Sci, 20,
908-924.
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PDB code:
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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.
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Nucleic Acids Res, 38,
4527-4538.
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PDB code:
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J.Zhao,
Q.Li,
J.A.Lu,
and
Z.P.Jiang
(2010).
Topology identification of complex dynamical networks.
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Chaos, 20,
023119.
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M.Ali,
B.Buentello-Volante,
M.McKibbin,
J.A.Rocha-Medina,
N.Fernandez-Fuentes,
W.Koga-Nakamura,
A.Ashiq,
K.Khan,
A.P.Booth,
G.Williams,
Y.Raashid,
H.Jafri,
A.Rice,
C.F.Inglehearn,
and
J.C.Zenteno
(2010).
Homozygous FOXE3 mutations cause non-syndromic, bilateral, total sclerocornea, aphakia, microphthalmia and optic disc coloboma.
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Mol Vis, 16,
1162-1168.
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F.Sorrentino,
and
E.Ott
(2009).
Using synchronism of chaos for adaptive learning of time-evolving network topology.
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Phys Rev E Stat Nonlin Soft Matter Phys, 79,
016201.
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S.Hannenhalli,
and
K.H.Kaestner
(2009).
The evolution of Fox genes and their role in development and disease.
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Nat Rev Genet, 10,
233-240.
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A.Costa,
G.van Duinen,
B.Medagli,
J.Chong,
N.Sakakibara,
Z.Kelman,
S.K.Nair,
A.Patwardhan,
and
S.Onesti
(2008).
Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase.
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EMBO J, 27,
2250-2258.
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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.
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Hum Mol Genet, 17,
3118-3127.
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M.M.Brent,
R.Anand,
and
R.Marmorstein
(2008).
Structural basis for DNA recognition by FoxO1 and its regulation by posttranslational modification.
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Structure, 16,
1407-1416.
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PDB codes:
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S.Schneider,
W.Zhang,
P.Soultanas,
and
M.Paoli
(2008).
Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation.
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J Mol Biol, 376,
1237-1250.
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PDB code:
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Z.Zhou,
X.Song,
B.Li,
and
M.I.Greene
(2008).
FOXP3 and its partners: structural and biochemical insights into the regulation of FOXP3 activity.
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Immunol Res, 42,
19-28.
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E.Boura,
J.Silhan,
P.Herman,
J.Vecer,
M.Sulc,
J.Teisinger,
V.Obsilova,
and
T.Obsil
(2007).
Both the N-terminal loop and wing W2 of the forkhead domain of transcription factor Foxo4 are important for DNA binding.
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J Biol Chem, 282,
8265-8275.
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G.Navarro-Avilés,
M.A.Jiménez,
M.C.Pérez-Marín,
C.González,
M.Rico,
F.J.Murillo,
M.Elías-Arnanz,
and
S.Padmanabhan
(2007).
Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor.
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Mol Microbiol, 63,
980-994.
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PDB code:
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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.
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Nucleic Acids Res, 35,
6984-6994.
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L.A.Cirillo,
and
K.S.Zaret
(2007).
Specific interactions of the wing domains of FOXA1 transcription factor with DNA.
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J Mol Biol, 366,
720-724.
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S.Yaklichkin,
A.B.Steiner,
Q.Lu,
and
D.S.Kessler
(2007).
FoxD3 and Grg4 physically interact to repress transcription and induce mesoderm in Xenopus.
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J Biol Chem, 282,
2548-2557.
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J.C.Stroud,
Y.Wu,
D.L.Bates,
A.Han,
K.Nowick,
S.Paabo,
H.Tong,
and
L.Chen
(2006).
Structure of the forkhead domain of FOXP2 bound to DNA.
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Structure, 14,
159-166.
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PDB code:
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K.L.Tsai,
C.Y.Huang,
C.H.Chang,
Y.J.Sun,
W.J.Chuang,
and
C.D.Hsiao
(2006).
Crystal structure of the human FOXK1a-DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins.
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J Biol Chem, 281,
17400-17409.
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PDB code:
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R.J.Maraia,
and
M.A.Bayfield
(2006).
The La protein-RNA complex surfaces.
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Mol Cell, 21,
149-152.
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B.S.Pohl,
and
W.Knöchel
(2005).
Of Fox and Frogs: Fox (fork head/winged helix) transcription factors in Xenopus development.
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Gene, 344,
21-32.
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M.Devany,
N.P.Kotharu,
and
H.Matsuo
(2004).
Solution NMR structure of the C-terminal domain of the human protein DEK.
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Protein Sci, 13,
2252-2259.
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PDB code:
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R.A.Saleem,
S.Banerjee-Basu,
T.C.Murphy,
A.Baxevanis,
and
M.A.Walter
(2004).
Essential structural and functional determinants within the forkhead domain of FOXC1.
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Nucleic Acids Res, 32,
4182-4193.
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S.Banerjee-Basu,
and
A.D.Baxevanis
(2004).
Structural analysis of disease-causing mutations in the P-subfamily of forkhead transcription factors.
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Proteins, 54,
639-647.
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H.Yan,
and
X.Liao
(2003).
Amino acid substitutions in a long flexible sequence influence thermodynamics and internal dynamic properties of winged helix protein genesis and its DNA complex.
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Biophys J, 85,
3248-3254.
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K.Ono,
O.Kusano,
S.Shimotakahara,
M.Shimizu,
T.Yamazaki,
and
H.Shindo
(2003).
The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy.
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Nucleic Acids Res, 31,
7199-7207.
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PDB code:
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N.Mizuno,
G.Voordouw,
K.Miki,
A.Sarai,
and
Y.Higuchi
(2003).
Crystal structure of dissimilatory sulfite reductase D (DsrD) protein--possible interaction with B- and Z-DNA by its winged-helix motif.
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Structure, 11,
1133-1140.
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PDB code:
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T.Obsil,
R.Ghirlando,
D.E.Anderson,
A.B.Hickman,
and
F.Dyda
(2003).
Two 14-3-3 binding motifs are required for stable association of Forkhead transcription factor FOXO4 with 14-3-3 proteins and inhibition of DNA binding.
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Biochemistry, 42,
15264-15272.
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P.P.Liu,
Y.C.Chen,
C.Li,
Y.H.Hsieh,
S.W.Chen,
S.H.Chen,
W.Y.Jeng,
and
W.J.Chuang
(2002).
Solution structure of the DNA-binding domain of interleukin enhancer binding factor 1 (FOXK1a).
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Proteins, 49,
543-553.
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PDB code:
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S.Ramaswamy,
N.Nakamura,
I.Sansal,
L.Bergeron,
and
W.R.Sellers
(2002).
A novel mechanism of gene regulation and tumor suppression by the transcription factor FKHR.
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Cancer Cell, 2,
81-91.
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W.Sheng,
M.Rance,
and
X.Liao
(2002).
Structure comparison of two conserved HNF-3/fkh proteins HFH-1 and genesis indicates the existence of folding differences in their complexes with a DNA binding sequence.
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Biochemistry, 41,
3286-3293.
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PDB code:
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J.Weigelt,
I.Climent,
K.Dahlman-Wright,
and
M.Wikström
(2001).
Solution structure of the DNA binding domain of the human forkhead transcription factor AFX (FOXO4).
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Biochemistry, 40,
5861-5869.
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M.H.Godsey,
N.N.Baranova,
A.A.Neyfakh,
and
R.G.Brennan
(2001).
Crystal structure of MtaN, a global multidrug transporter gene activator.
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J Biol Chem, 276,
47178-47184.
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PDB code:
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R.A.Saleem,
S.Banerjee-Basu,
F.B.Berry,
A.D.Baxevanis,
and
M.A.Walter
(2001).
Analyses of the effects that disease-causing missense mutations have on the structure and function of the winged-helix protein FOXC1.
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Am J Hum Genet, 68,
627-641.
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T.Stockner,
C.Plugariu,
G.Koraimann,
G.Högenauer,
W.Bermel,
S.Prytulla,
and
H.Sterk
(2001).
Solution structure of the DNA-binding domain of TraM.
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Biochemistry, 40,
3370-3377.
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PDB code:
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K.S.Gajiwala,
and
S.K.Burley
(2000).
Winged helix proteins.
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Curr Opin Struct Biol, 10,
110-116.
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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.
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Links
