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PDBsum entry 1jm0
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De novo protein
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PDB id
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1jm0
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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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Toward the de novo design of a catalytically active helix bundle: a substrate-Accessible carboxylate-Bridged dinuclear metal center.
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Authors
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L.Di costanzo,
H.Wade,
S.Geremia,
L.Randaccio,
V.Pavone,
W.F.Degrado,
A.Lombardi.
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Ref.
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J Am Chem Soc, 2001,
123,
12749-12757.
[DOI no: ]
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PubMed id
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Abstract
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De novo design of proteins provides an attractive approach to uncover the
essential features required for their functions. Previously, we described the
design and crystal structure determination of a di-Zn(II) complex of
"due-ferri-1" (DF1), a protein patterned after the diiron-dimanganese class of
redox-active proteins [Lombardi, A.; Summa, C.; Geremia, S.; Randaccio, L.;
Pavone, V.; DeGrado, W. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6298-6305].
The overall structure of DF1, which contains a carboxylate-bridged dinuclear
metal site, agrees well with the intended design. However, access to this
dimetal site is blocked by a pair of hydrophobic leucine residues (L13 and
L13'), which prevent facile entry of metal ions and small molecules. We have now
taken the next step in the eventual construction of a catalytically active
metalloenzyme by engineering an active site cavity into DF1 through the
replacement of these two leucine residues with smaller residues. The crystal
structure of the dimanganous form of L13A-DF1 indeed shows a substrate access
channel to the dimetal center. In the crystal structure, water molecules and a
ligating dimethyl sulfoxide molecule, which forms a monatomic bridge between the
metal ions, occupy the cavity. Furthermore, the diferric form of a derivative of
L13A-DF1, DF2, is shown to bind azide, acetate, and small aromatic molecules.
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Secondary reference #1
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Title
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Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
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Authors
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A.Lombardi,
C.M.Summa,
S.Geremia,
L.Randaccio,
V.Pavone,
W.F.Degrado.
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Ref.
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Proc Natl Acad Sci U S A, 2000,
97,
6298-6305.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Structure of dimetal ion site in an idealized
diiron protein. Two Glu side chains form a bridging interaction
between the metal ions, whereas the remaining two carboxylates
form a one- or two-coordinate interaction with a single metal
ion. Two His side chains are visible behind the ions. Two vacant
sites face the viewer and are trans to the His ligands (Right).
The figure shows the crystal structure of DF1; carbon atoms are
green, nitrogens are blue, oxygens are red, and metal ions are
magenta. The backbone trace is shown in purple.
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Figure 4.
Fig. 4. Stereo comparison of 2.5 Å di-Zn-DF1
structure with designed model. The superposition of the crystal
structure symmetric dimer (green) and the designed model (gray)
shows the liganding Glu and His residues. Note that the
dimetal-binding site is nearly identical between the model and
the crystal structure. However, conformation of the Tyr-2 and
Trp-42 side chains in the crystal structure differs markedly
from that in the design.
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Secondary reference #2
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Title
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Tertiary templates for the design of diiron proteins.
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Authors
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C.M.Summa,
A.Lombardi,
M.Lewis,
W.F.Degrado.
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Ref.
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Curr Opin Struct Biol, 1999,
9,
500-508.
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PubMed id
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Secondary reference #3
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Title
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De novo design and structural characterization of proteins and metalloproteins.
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Authors
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W.F.Degrado,
C.M.Summa,
V.Pavone,
F.Nastri,
A.Lombardi.
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Ref.
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Annu Rev Biochem, 1999,
68,
779-819.
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PubMed id
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