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PDBsum entry 1hdd
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Transcription/DNA
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PDB id
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1hdd
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Contents |
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* Residue conservation analysis
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DOI no:
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Cell
63:579-590
(1990)
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PubMed id:
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Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.
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C.R.Kissinger,
B.S.Liu,
E.Martin-Blanco,
T.B.Kornberg,
C.O.Pabo.
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ABSTRACT
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The crystal structure of a complex containing the engrailed homeodomain and a
duplex DNA site has been determined at 2.8 A resolution and refined to a
crystallographic R factor of 24.4%. In this complex, two separate regions of the
61 amino acid polypeptide contact a TAAT subsite. An N-terminal arm fits into
the minor groove, and the side chains of Arg-3 and Arg-5 make contacts near the
5' end of this "core consensus" binding site. An alpha helix fits into
the major groove, and the side chains of IIe-47 and Asn-51 contact base pairs
near the 3' end of the TAAT site. This "recognition helix" is part of
a structurally conserved helix-turn-helix unit, but these helices are longer
than the corresponding helices in the lambda repressor, and the relationship
between the helix-turn-helix unit and the DNA is significantly different.
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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.C.Harris,
M.Hrmova,
S.Lopato,
and
P.Langridge
(2011).
Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli.
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New Phytol,
190,
823-837.
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Z.Xie,
S.Hu,
J.Qian,
S.Blackshaw,
and
H.Zhu
(2011).
Systematic characterization of protein-DNA interactions.
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Cell Mol Life Sci,
68,
1657-1668.
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C.S.Suh,
S.Ellingsen,
L.Austbø,
X.F.Zhao,
H.C.Seo,
and
A.Fjose
(2010).
Autoregulatory binding sites in the zebrafish six3a promoter region define a new recognition sequence for Six3 proteins.
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FEBS J,
277,
1761-1775.
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H.M.Lee,
H.Zhang,
V.Schulz,
D.P.Tuck,
and
B.G.Forget
(2010).
Downstream targets of HOXB4 in a cell line model of primitive hematopoietic progenitor cells.
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Blood,
116,
720-730.
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H.Neuweiler,
W.Banachewicz,
and
A.R.Fersht
(2010).
Kinetics of chain motions within a protein-folding intermediate.
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Proc Natl Acad Sci U S A,
107,
22106-22110.
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L.Marchetti,
L.Comelli,
B.D'Innocenzo,
L.Puzzi,
S.Luin,
D.Arosio,
M.Calvello,
R.Mendoza-Maldonado,
F.Peverali,
F.Trovato,
S.Riva,
G.Biamonti,
G.Abdurashidova,
F.Beltram,
and
A.Falaschi
(2010).
Homeotic proteins participate in the function of human-DNA replication origins.
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| |
Nucleic Acids Res,
38,
8105-8119.
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P.Agius,
A.Arvey,
W.Chang,
W.S.Noble,
and
C.Leslie
(2010).
High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
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PLoS Comput Biol,
6,
0.
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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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A.Shen,
D.E.Higgins,
and
D.Panne
(2009).
Recognition of AT-rich DNA binding sites by the MogR repressor.
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Structure,
17,
769-777.
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PDB code:
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C.Y.Yang,
K.H.Chin,
M.T.Yang,
A.H.Wang,
and
S.H.Chou
(2009).
Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris.
|
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Proteins,
74,
530-537.
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PDB code:
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R.Rohs,
S.M.West,
A.Sosinsky,
P.Liu,
R.S.Mann,
and
B.Honig
(2009).
The role of DNA shape in protein-DNA recognition.
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Nature,
461,
1248-1253.
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R.T.Moreland,
J.F.Ryan,
C.Pan,
and
A.D.Baxevanis
(2009).
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family.
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Database (Oxford),
2009,
bap004.
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T.M.Alleyne,
L.Peña-Castillo,
G.Badis,
S.Talukder,
M.F.Berger,
A.R.Gehrke,
A.A.Philippakis,
M.L.Bulyk,
Q.D.Morris,
and
T.R.Hughes
(2009).
Predicting the binding preference of transcription factors to individual DNA k-mers.
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Bioinformatics,
25,
1012-1018.
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Y.C.Lou,
S.Y.Wei,
M.Rajasekaran,
C.C.Chou,
H.M.Hsu,
J.H.Tai,
and
C.Chen
(2009).
NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis.
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Nucleic Acids Res,
37,
2381-2394.
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PDB codes:
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F.Alasti,
A.Sadeghi,
M.H.Sanati,
M.Farhadi,
E.Stollar,
T.Somers,
and
G.Van Camp
(2008).
A mutation in HOXA2 is responsible for autosomal-recessive microtia in an Iranian family.
|
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Am J Hum Genet,
82,
982-991.
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M.B.Noyes,
R.G.Christensen,
A.Wakabayashi,
G.D.Stormo,
M.H.Brodsky,
and
S.A.Wolfe
(2008).
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
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Cell,
133,
1277-1289.
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M.E.McCully,
D.A.Beck,
and
V.Daggett
(2008).
Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.
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Biochemistry,
47,
7079-7089.
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M.F.Berger,
G.Badis,
A.R.Gehrke,
S.Talukder,
A.A.Philippakis,
L.Peña-Castillo,
T.M.Alleyne,
S.Mnaimneh,
O.B.Botvinnik,
E.T.Chan,
F.Khalid,
W.Zhang,
D.Newburger,
S.A.Jaeger,
Q.D.Morris,
M.L.Bulyk,
and
T.R.Hughes
(2008).
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.
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Cell,
133,
1266-1276.
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P.K.Purbey,
S.Singh,
P.P.Kumar,
S.Mehta,
K.N.Ganesh,
D.Mitra,
and
S.Galande
(2008).
PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1.
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Nucleic Acids Res,
36,
2107-2122.
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T.L.Religa
(2008).
Comparison of multiple crystal structures with NMR data for engrailed homeodomain.
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J Biomol NMR,
40,
189-202.
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PDB code:
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C.G.Danko,
V.A.McIlvain,
M.Qin,
B.E.Knox,
and
A.M.Pertsov
(2007).
Bioinformatic identification of novel putative photoreceptor specific cis-elements.
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BMC Bioinformatics,
8,
407.
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D.A.Beck,
and
V.Daggett
(2007).
A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.
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Biophys J,
93,
3382-3391.
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E.F.Koslover,
and
D.J.Wales
(2007).
Geometry optimization for peptides and proteins: Comparison of Cartesian and internal coordinates.
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J Chem Phys,
127,
234105.
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E.Shacham,
B.Sheehan,
and
N.Volkmann
(2007).
Density-based score for selecting near-native atomic models of unknown structures.
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J Struct Biol,
158,
188-195.
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H.C.Park,
M.L.Kim,
S.M.Lee,
J.D.Bahk,
D.J.Yun,
C.O.Lim,
J.C.Hong,
S.Y.Lee,
M.J.Cho,
and
W.S.Chung
(2007).
Pathogen-induced binding of the soybean zinc finger homeodomain proteins GmZF-HD1 and GmZF-HD2 to two repeats of ATTA homeodomain binding site in the calmodulin isoform 4 (GmCaM4) promoter.
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Nucleic Acids Res,
35,
3612-3623.
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S.C.Harrison
(2007).
Three-dimensional intricacies in protein-DNA recognition and transcriptional control.
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Nat Struct Mol Biol,
14,
1118-1119.
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S.Mahony,
P.E.Auron,
and
P.V.Benos
(2007).
Inferring protein-DNA dependencies using motif alignments and mutual information.
|
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Bioinformatics,
23,
i297-i304.
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X.Zhao,
M.Sun,
J.Zhao,
J.A.Leyva,
H.Zhu,
W.Yang,
X.Zeng,
Y.Ao,
Q.Liu,
G.Liu,
W.H.Lo,
E.W.Jabs,
L.M.Amzel,
X.Shan,
and
X.Zhang
(2007).
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome.
|
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Am J Hum Genet,
80,
361-371.
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C.Crane-Robinson,
A.I.Dragan,
and
P.L.Privalov
(2006).
The extended arms of DNA-binding domains: a tale of tails.
|
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Trends Biochem Sci,
31,
547-552.
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F.Liu,
F.A.Ismat,
and
V.V.Patel
(2006).
Role of homeodomain-only protein in the cardiac conduction system.
|
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Trends Cardiovasc Med,
16,
193-198.
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J.Iwahara,
M.Zweckstetter,
and
G.M.Clore
(2006).
NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.
|
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Proc Natl Acad Sci U S A,
103,
15062-15067.
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S.Lim,
and
S.J.Franklin
(2006).
Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution.
|
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Protein Sci,
15,
2159-2165.
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T.Svingen,
and
K.F.Tonissen
(2006).
Hox transcription factors and their elusive mammalian gene targets.
|
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Heredity,
97,
88-96.
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W.Zhang,
B.Li,
R.Singh,
U.Narendra,
L.Zhu,
and
M.A.Weiss
(2006).
Regulation of sexual dimorphism: mutational and chemogenetic analysis of the doublesex DM domain.
|
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Mol Cell Biol,
26,
535-547.
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Y.Choi,
and
A.Rajkovic
(2006).
Characterization of NOBOX DNA binding specificity and its regulation of Gdf9 and Pou5f1 promoters.
|
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J Biol Chem,
281,
35747-35756.
|
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D.Lebrecht,
M.Foehr,
E.Smith,
F.J.Lopes,
C.E.Vanario-Alonso,
J.Reinitz,
D.S.Burz,
and
S.D.Hanes
(2005).
Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila.
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Proc Natl Acad Sci U S A,
102,
13176-13181.
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D.Sikder,
and
T.Kodadek
(2005).
Genomic studies of transcription factor-DNA interactions.
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Curr Opin Chem Biol,
9,
38-45.
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F.Zhu,
Z.C.Liu,
W.X.Li,
and
X.L.Xu
(2005).
Rapid identification of Quox-1 homeodomain DNA-binding sequence using SAAB.
|
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Biochemistry (Mosc),
70,
920-925.
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K.U.Schneider,
A.Marchini,
N.Sabherwal,
R.Röth,
B.Niesler,
T.Marttila,
R.J.Blaschke,
M.Lawson,
M.Dumic,
and
G.Rappold
(2005).
Alteration of DNA binding, dimerization, and nuclear translocation of SHOX homeodomain mutations identified in idiopathic short stature and Leri-Weill dyschondrosteosis.
|
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Hum Mutat,
26,
44-52.
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M.F.Tioni,
I.L.Viola,
R.L.Chan,
and
D.H.Gonzalez
(2005).
Site-directed mutagenesis and footprinting analysis of the interaction of the sunflower KNOX protein HAKN1 with DNA.
|
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FEBS J,
272,
190-202.
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M.S.Yousef,
and
B.W.Matthews
(2005).
Structural basis of Prospero-DNA interaction: implications for transcription regulation in developing cells.
|
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Structure,
13,
601-607.
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PDB code:
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M.Saviano,
C.Isernia,
C.Bassarello,
P.Di Lello,
S.Galdiero,
D.F.Mierke,
E.Benedetti,
and
C.Pedone
(2005).
Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain.
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J Pept Res,
65,
200-208.
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A.Liberzon,
G.Ridner,
and
M.D.Walker
(2004).
Role of intrinsic DNA binding specificity in defining target genes of the mammalian transcription factor PDX1.
|
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Nucleic Acids Res,
32,
54-64.
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B.Mollé,
S.Père,
V.Failli,
I.Bach,
and
S.Rétaux
(2004).
Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation.
|
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DNA Cell Biol,
23,
761-768.
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H.B.Abdelkhalek,
A.Beckers,
K.Schuster-Gossler,
M.N.Pavlova,
H.Burkhardt,
H.Lickert,
J.Rossant,
R.Reinhardt,
L.C.Schalkwyk,
I.Müller,
B.G.Herrmann,
M.Ceolin,
R.Rivera-Pomar,
and
A.Gossler
(2004).
The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation.
|
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Genes Dev,
18,
1725-1736.
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H.DU,
and
H.S.Taylor
(2004).
Molecular regulation of mullerian development by Hox genes.
|
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Ann N Y Acad Sci,
1034,
152-165.
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H.H.Simon,
S.Thuret,
and
L.Alberi
(2004).
Midbrain dopaminergic neurons: control of their cell fate by the engrailed transcription factors.
|
| |
Cell Tissue Res,
318,
53-61.
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M.D.Simon,
K.Sato,
G.A.Weiss,
and
K.M.Shokat
(2004).
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50.
|
| |
Nucleic Acids Res,
32,
3623-3631.
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U.Vijapurkar,
N.Fischbach,
W.Shen,
C.Brandts,
D.Stokoe,
H.J.Lawrence,
and
C.Largman
(2004).
Protein kinase C-mediated phosphorylation of the leukemia-associated HOXA9 protein impairs its DNA binding ability and induces myeloid differentiation.
|
| |
Mol Cell Biol,
24,
3827-3837.
|
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W.Shen,
D.Chrobak,
K.Krishnan,
H.J.Lawrence,
and
C.Largman
(2004).
HOXB6 protein is bound to CREB-binding protein and represses globin expression in a DNA binding-dependent, PBX interaction-independent process.
|
| |
J Biol Chem,
279,
39895-39904.
|
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Y.Hashimoto,
O.Tsuji,
K.Kanekura,
S.Aiso,
T.Niikura,
M.Matsuoka,
and
I.Nishimoto
(2004).
The Gtx homeodomain transcription factor exerts neuroprotection using its homeodomain.
|
| |
J Biol Chem,
279,
16767-16777.
|
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A.Ke,
and
C.Wolberger
(2003).
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.
|
| |
Protein Sci,
12,
306-312.
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PDB codes:
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D.W.Kim,
H.Kempf,
R.E.Chen,
and
A.B.Lassar
(2003).
Characterization of Nkx3.2 DNA binding specificity and its requirement for somitic chondrogenesis.
|
| |
J Biol Chem,
278,
27532-27539.
|
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E.J.Stollar,
U.Mayor,
S.C.Lovell,
L.Federici,
S.M.Freund,
A.R.Fersht,
and
B.F.Luisi
(2003).
Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics.
|
| |
J Biol Chem,
278,
43699-43708.
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PDB codes:
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E.S.Baekkevold,
M.Roussigné,
T.Yamanaka,
F.E.Johansen,
F.L.Jahnsen,
F.Amalric,
P.Brandtzaeg,
M.Erard,
G.Haraldsen,
and
J.P.Girard
(2003).
Molecular characterization of NF-HEV, a nuclear factor preferentially expressed in human high endothelial venules.
|
| |
Am J Pathol,
163,
69-79.
|
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K.J.Hwang,
B.Xiang,
J.M.Gruschus,
K.Y.Nam,
K.T.No,
M.Nirenberg,
and
J.A.Ferretti
(2003).
Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.
|
| |
Biochemistry,
42,
12522-12531.
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PDB code:
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S.Banerjee-Basu,
T.Moreland,
B.J.Hsu,
K.L.Trout,
and
A.D.Baxevanis
(2003).
The Homeodomain Resource: 2003 update.
|
| |
Nucleic Acids Res,
31,
304-306.
|
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X.Bi,
A.V.Kajava,
T.Jones,
Z.N.Demidenko,
and
M.A.Mortin
(2003).
The carboxy terminus of Prospero regulates its subcellular localization.
|
| |
Mol Cell Biol,
23,
1014-1024.
|
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A.E.Tron,
C.W.Bertoncini,
R.L.Chan,
and
D.H.Gonzalez
(2002).
Redox regulation of plant homeodomain transcription factors.
|
| |
J Biol Chem,
277,
34800-34807.
|
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A.Ke,
J.R.Mathias,
A.K.Vershon,
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PDB code:
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Where a reference describes a PDB structure, the PDB
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|
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