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PDBsum entry 2w3u
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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 ni(ii) complex of escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(ii) centres.
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Authors
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N.T.Yen,
X.Bogdanović,
G.J.Palm,
O.Kühl,
W.Hinrichs.
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Ref.
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J Biol Inorg Chem, 2010,
15,
195-201.
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PubMed id
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Abstract
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Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with
nickel(II) replacing the native iron(II) have been solved with chloride and
formate as metal ligands. The chloro complex is a model for the correct
protonation state of the hydrolytic hydroxo ligand and the protonated status of
the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that
recently some PDFs have been identified with Zn(2+) ion as the active-site
centre whereas others are only active with Fe(2+) (or Co(2+), Ni(2+) is
discussed with respect to Lewis acid criteria of the metal ion and substrate
activation by the CD loop.
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Secondary reference #1
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Title
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Iron center, Substrate recognition and mechanism of peptide deformylase.
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Authors
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A.Becker,
I.Schlichting,
W.Kabsch,
D.Groche,
S.Schultz,
A.F.Wagner.
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Ref.
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Nat Struct Biol, 1998,
5,
1053-1058.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. a, Omit map of Met-Ala-Ser in the PDF−Ni/MAS
structure contoured at 1  .
Figure prepared with BobScript^25. b, Stereo-view of
superimposed C  -traces
of the three crystallographically independent copies of peptide
deformylase in complex with the reaction product Met-Ala-Ser.
The numbers refer to amino acid residues. The transformations
for optimal superposition were determined from equivalent C -atoms
using molecule A as a reference and applied to the Ni^2+ ion
(marked as Ni) and the peptide as well. Molecule complexes A, B,
C are shown in green, magenta, blue, respectively. c, Active
site of PDF−Ni (monomer A) with bound catalytic product
Met-Ala-Ser, ordered water molecules W1, W2 and the Ni^2+ ion.
d, A hypothetical model of PDF with bound substrate
formyl-Met-Ala-Ser.
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Figure 2.
Figure 2. Peptide deformylase in complex with the reaction
product Met-Ala-Ser. a, Peptide binding scheme; Gly 45, Glu
88, Gly 89, His 132 and Glu 133 are conserved residues. Dashed
lines indicate hydrogen bonds. Mean distances between donor and
acceptor atoms as observed in the three crystallographically
independent monomers are given in Å . The distance between
the N-terminal amino group of the peptide to the Ni^2+-ion is
 3.9
Å. b, Protein atoms (white, carbon; red, oxygen; dark
blue, nitrogen; green, sulphur) and catalytic metal (magenta,
Ni^2+) are depicted as space-filling spheres. Met-Ala-Ser is in
ball-and-stick representation with carbon atoms and bonds
colored yellow. Water molecules W1, W2 are shown as small light
blue spheres. Figure prepared using MOLSCRIPT^26 and Raster3D^27.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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