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PDBsum entry 1n0r
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Structural protein
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PDB id
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1n0r
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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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Consensus-Derived structural determinants of the ankyrin repeat motif.
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Authors
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L.K.Mosavi,
D.L.Minor,
Z.Y.Peng.
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Ref.
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Proc Natl Acad Sci U S A, 2002,
99,
16029-16034.
[DOI no: ]
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PubMed id
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Abstract
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The ankyrin repeat is one of the most common, modular, protein-protein
interaction motifs in nature. To understand the structural determinants of this
family of proteins and extract the consensus information that defines the
architecture of this motif, we have designed a series of idealized ankyrin
repeat proteins containing one, two, three, or four repeats by using statistical
analysis of approximately 4,000 ankyrin repeat sequences from the PFAM database.
Biophysical and x-ray crystallographic studies of the three and four repeat
constructs (3ANK and 4ANK) to 1.26 and 1.5 A resolution, respectively,
demonstrate that these proteins are well-folded, monomeric, display high
thermostability, and adopt a very regular, tightly packed ankyrin repeat fold.
Mapping the degree of amino acid conservation at each position on the 4ANK
structure shows that most nonconserved residues are clustered on the surface of
the molecule that has been designated as the binding site in naturally occurring
ankyrin repeat proteins. Thus, the consensus amino acid sequence contains all
information required to define the ankyrin repeat fold. Our results suggest that
statistical analysis and the consensus sequence approach can be used as an
effective method to design proteins with complex topologies. These generic
ankyrin repeat proteins can serve as prototypes for dissecting the rules of
molecular recognition mediated by ankyrin repeats and for engineering proteins
with novel biological functions.
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Figure 3.
Fig 3. X-ray crystal structures of 3ANK and 4ANK. (a)
Stereo representation showing the initial electron density map
of residues 37-40 of 4ANK, including the TPLH motif, contoured
at 1.5  . The figure was made
with O and rendered by using MOLRAY (43). (b) Overlay of 3ANK
(cyan) and 4ANK (orange) backbone structures. This figure and
all following structural representations were made with MOLMOL
(44). (c) Hydrogen bonding network in  -hairpin/loop region of
4ANK. Each repeat is colored differently and hydrogen bonds are
represented by letters: a, D32(OD1) and N34(HN); b, D32(O) and
G35(HN); c, D32(OD1) and R36(HN); d, D32(HN) and R36(O); e,
R36(O) and H7(HNE2); f, A30(O) and H7(HNE2); g, A30(HN) and
D27(O); h, D27(OD1) and N29(HN); i, N29(OD1) and D60(HN); j,
N29(ND2) and G58(O); k, N34(O) and K66(HN); and l, R36(HNE) and
D65(OD2). Equivalent hydrogen bonds in adjacent repeats are
represented by the letter followed by ' or " and for all residue
numbers i > 33, the canonical ankyrin repeat position = i - 33.
(d) Comparison of intramolecular packing of ankyrin repeat
proteins based on the occluded surface area analysis. For each
protein, the average ray length of all residues was plotted
against the average occluded surface packing (OSP) value of all
buried residues with exposed surface area of <5%. The average
values of 152 high-resolution structures in PDB are shown by the
dashed lines on the graph (31).
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Figure 4.
Fig 4. Conservation level of residues mapped onto the
structure of 4ANK. Colors represent the conservation level:
blue, well-conserved; pink, semiconserved of the same type;
green, semiconserved of different type; and yellow,
nonconserved. The C-terminal tyrosine is colored in gray. (a)
Front (concave) surface of 4ANK. (b) Back surface of 4ANK. The
ribbon diagrams on the left show orientations. (c) Longitudinal
cross-section of the protein displaying the interior residues.
Protein is in the same orientation as in b.
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