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PDBsum entry 1d1c
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Contractile protein
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PDB id
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1d1c
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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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X-Ray structures of the dictyostelium discoideum myosin motor domain with six non-Nucleotide analogs.
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Authors
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A.M.Gulick,
C.B.Bauer,
J.B.Thoden,
E.Pate,
R.G.Yount,
I.Rayment.
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Ref.
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J Biol Chem, 2000,
275,
398-408.
[DOI no: ]
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PubMed id
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Abstract
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The three-dimensional structures of the truncated myosin head from Dictyostelium
discoideum myosin II complexed with dinitrophenylaminoethyl-,
dinitrophenylaminopropyl-, o-nitrophenylaminoethyl-, m-nitrophenylaminoethyl-,
p-nitrophenylaminoethyl-, and
o-nitrophenyl-N-methyl-aminoethyl-diphosphate.beryllium fluoride have been
determined to better than 2.3-A resolution. The structure of the protein and
nucleotide binding pocket in these complexes is very similar to that of
S1dC.ADP.BeF(x) (Fisher, A. J., Smith, C. A., Thoden, J., Smith, R., Sutoh, K.,
Holden, H. M., and Rayment, I. (1995) Biochemistry 34, 8960-8972). The position
of the triphosphate-like moiety is essentially identical in all complexes.
Furthermore, the alkyl-amino group plays the same role as the ribose by linking
the triphosphate to the adenine binding pocket; however, none of the phenyl
groups lie in the same position as adenine in S1dC.MgADP.BeF(x), even though
several of these nucleotide analogs are functionally equivalent to ATP. Rather
the former location of adenine is occupied by water in the nanolog complexes,
and the phenyl groups are organized in a manner that attempts to optimize their
hydrogen bonding interactions with this constellation of solvent molecules. A
comparison of the kinetic and structural properties of the nanologs relative to
ATP suggests that the ability of a substrate to sustain tension and to generate
movement correlates with a well defined interaction with the active site water
structure observed in S1dC.MgADP.BeF(x).
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Figure 1.
Fig. 1. Electron density for the nucleotide analogs.
Stereodiagrams are shown for the active site contents of the
complexes of the six nanologs with S1dC as follows: a, o-NPhAE;
b, m-NPhAE; c, p-NPhAE; d, o,p-NPhAE; e, o,p-DNPhAP; f,
N-methyl-NPhAE. The nanologs and Mg2+ atoms were removed from
the coordinate file, and the structure was submitted to one
round of least squares refinement with TNT (31). The subsequent
omit map, created with coefficients of the form F[o]  F[c], was
contoured at 2.5  and used
to create the figures. The residues that form the P-loop which
wraps around the triphosphate region of the nucleotide,
Ser181-Asn188, are shown as ball and stick. Additionally, the
N-terminal region that forms the binding pocket for the
nucleotide (Asn127-Pro133) is included. The side chains for
Asn127, Phe^129, and Arg131 are represented with ball and stick
atoms. The atoms are colored by atom type for the nanologs as
follows: carbon, gray; oxygen, red; nitrogen, blue; beryllium,
green; fluorine, yellow; phosphorus, magenta; and magnesium,
orange. All protein atoms are colored gray. Figs. 1-4 were
prepared with the programs Molscript and Molded (18, 54).
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Figure 2.
Fig. 2. Location of the nanolog molecule within the
active site. The orientations of the nanolog molecules compared
with ADP·BeF[x] are shown. a shows the adenine base of
ADP located in the base pocket that is formed by residues
Asn127-Tyr135. The coordinates for this figure were taken from
1MMD (17). c, the ATP nucleotide molecule is shown as ball and
stick with yellow bonds. The colors of specific atoms are as in
Fig. 1. The nanolog molecules are superimposed on the molecule
of ADP·BeF[x] and are represented in solid colors. b,
o-NPhAE, m-NPhAE, and p-NPhAE are shown in orange, cyan, and
magenta, respectively. c, o,p-DNPhAE, o,p-DNPhAP, and
N-methyl-NPhAE are shown in purple, red, and green,
respectively. The protein backbones were aligned with the
program LSQKAB implemented in the CCP4 program package (33, 41)
where all  carbons
were included in the calculation.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
398-408)
copyright 2000.
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