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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.
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PubMed id
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Abstract
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Eubacterial proteins are synthesized with a formyl group at the N-terminus which
is hydrolytically removed from the nascent chain by the mononuclear iron enzyme
peptide deformylase. Catalytic efficiency strongly depends on the identity of
the bound metal. We have determined by X-ray crystallography the Fe2+, Ni2+ and
Zn2+ forms of the Escherichia coli enzyme and a structure in complex with the
reaction product Met-Ala-Ser. The structure of the complex, with the tripeptide
bound at the active site, suggests detailed models for the mechanism of
substrate recognition and catalysis. Differences of the protein structures due
to the identity of the bound metal are extremely small and account only for the
observation that Zn2+ binds more tightly than Fe2+ or Ni2+. The striking loss of
catalytic activity of the Zn2+ form could be caused by its reluctance to change
between tetrahedral and five-fold metal coordination believed to occur during
catalysis. N-terminal formylation and subsequent deformylation
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