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PDBsum entry 1odh
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Transcription factor/DNA
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PDB id
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1odh
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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 gcm domain-Dna complex: a DNA-Binding domain with a novel fold and mode of target site recognition.
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Authors
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S.X.Cohen,
M.Moulin,
S.Hashemolhosseini,
K.Kilian,
M.Wegner,
C.W.Müller.
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Ref.
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EMBO J, 2003,
22,
1835-1845.
[DOI no: ]
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PubMed id
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Abstract
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Glia cell missing (GCM) transcription factors form a small family of
transcriptional regulators in metazoans. The prototypical Drosophila GCM protein
directs the differentiation of neuron precursor cells into glia cells, whereas
mammalian GCM proteins are involved in placenta and parathyroid development. GCM
proteins share a highly conserved 150 amino acid residue region responsible for
DNA binding, known as the GCM domain. Here we present the crystal structure of
the GCM domain from murine GCMa bound to its octameric DNA target site at 2.85 A
resolution. The GCM domain exhibits a novel fold consisting of two domains
tethered together by one of two structural Zn ions. We observe the novel use of
a beta-sheet in DNA recognition, whereby a five- stranded beta-sheet protrudes
into the major groove perpendicular to the DNA axis. The structure combined with
mutational analysis of the target site and of DNA-contacting residues provides
insight into DNA recognition by this new type of Zn-containing DNA-binding
domain.
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Figure 2.
Figure 2 Structure of the GCM domain. (A) Ribbon representation
of the GCM domain bound to its cognate DNA. The  -sheets
of the large and small domains are depicted in dark blue and
light blue, respectively. Helices H1, H2 and H3 are shown in
red, and the DNA is shown in yellow. The two Zn ions and their
coordinating ligands are depicted. Figures 2A and B, 3B, 4A and
6 were produced using the program RIBBONS (Carson, 1991). (B)
View of the GCM domain with the DNA axis running vertically. DNA
bases are numbered according to Figure 1B. (C) Topology diagram
of the GCM domain. DNA-contacting residues and the first and
second Zn ion coordinating residues are marked as dots. The
color code corresponds to Figures 1A and 2A.
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Figure 3.
Figure 3 DNA recognition by the GCM domain. (A) Protein -DNA
interactions between the GCM domain and its DNA target site.
Arrows and dotted lines indicate polar and hydrophobic
interactions, respectively. Residues involved in polar and
hydrophobic interactions are drawn on blue and magenta
backgrounds, respectively. (B) Ribbon representation of the
interactions between the GCM domain and its DNA target site
Upper and lower strands as shown in Figure 1B are depicted in
yellow and orange, respectively. Broken lines indicate polar
interactions.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2003,
22,
1835-1845)
copyright 2003.
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