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PDBsum entry 2lfb
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References listed in PDB file
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Key reference
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Title
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The nmr solution structure of the non-Classical homeodomain from the rat liver lfb1/hnf1 transcription factor.
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Authors
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O.Schott,
M.Billeter,
B.Leiting,
G.Wider,
K.Wüthrich.
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Ref.
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J Mol Biol, 1997,
267,
673-683.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
95%.
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Abstract
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The nuclear magnetic resonance (NMR) solution structure of the non-classical
homeodomain from the rat liver LFB1/HNF1 transcription factor was determined
with the program DIANA from an input of 1356 nuclear Overhauser enhancement
(NOE) upper distance constraints and 228 dihedral angle constraints collected
using experiments with the unlabelled, the uniformly 15N-labelled and the
uniformly 13C-labelled protein. Out of a group of 50 independently calculated
conformers the 20 conformers with the smallest residual DIANA target function
values were refined by energy minimization with the program OPAL and are used to
represent the NMR structure. The average of the pairwise root-mean-square
deviations (r.m.s.d.) of these 20 individual NMR conformers relative to the mean
coordinates is 0.73 A (1 A = 0.1 nm) for the backbone atoms N, C(alpha) and C'
of residues 15 to 82. The chain-terminal polypeptide segments 1-14 and 90-99 are
disordered in solution. The globular fold contains three well-defined helices
comprising the residues 19 to 29, 37 to 53 and 71 to 81, and the third helix is
extended by a less well-ordered fourth helix with residues 82 to 89, which
coincides with corresponding observations in "classical" homeodomains.
Side-chain analysis resulted in 33 "best-defined" side-chains, with global
displacements smaller than 1.1 A, and addition of these side-chains to the
global superposition of residues 15 to 82 resulted in a r.m.s.d of 0.81 A. The
protein contains two hydrophobic cores, one of which corresponds to the helical
packing seen in classical homeodomains, while the other one stabilizes the
conformation of the 21-residue insertion between helices II and III. The
individual helices and their relative spatial arrangements are stabilized by a
variety of structural motifs, which include medium-range and long-range hydrogen
bonds and salt bridges. Detailed comparison with the Antennapedia homeodomain,
and studies of the complex formation with an operator DNA half-site provided
initial information on the DNA-binding mode of the LFB1/HNF1 homeodomain.
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Figure 6.
Figure 6. Hydrogen bonding interactions, salt bridges
and cation.p interactions that stabilize the global fold
of the LFB1/HNF1-homeodomain. Same presentation as
in Figure 5. The following specific interactions are
shown: the hydrogen bond H
d2
Asn47.O0 Val69, cation-
p interactions between the guanidinium group of Arg73
and the aromatic ring of Phe14, the hydrogen bond H
e
Gln26.O
e
Glu45, cation.p interactions between the gua-
nidinium group of Arg81 and the aromatic rings of
Trp77 and Tyr28, a salt bridge between the side-chains
of Arg81 and Glu85, and a hydrogen bond O
e
Glu85.
H
Z
Tyr28.
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Figure 7.
Figure 7. Comparison of the NMR solution structure
and the X-ray crystal structure of the LFB1/HNF1-
homeodomains. The backbones of the mean solution
structure and the crystal structure are shown as cyan
and red tubes, respectively. Only residues 15 to 89 are
shown, since the N and C-terminal ends 1 to 14 and 90
to 99 are disordered in solution, and have not been
reported in the crystal structure. The 33 side-chains
which are ``best-defined'' in the NMR structure (see
footnote to Table 2) are shown in yellow for the solution
structure and green for the crystal structure.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1997,
267,
673-683)
copyright 1997.
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Secondary reference #1
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Title
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The three-Dimensional nmr-Solution structure of the polypeptide fragment 195-286 of the lfb1/hnf1 transcription factor from rat liver comprises a nonclassical homeodomain.
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Authors
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B.Leiting,
R.De francesco,
L.Tomei,
R.Cortese,
G.Otting,
K.Wüthrich.
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Ref.
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Embo J, 1993,
12,
1797-1803.
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PubMed id
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