Structure of the Ni(II) complex of Escherichia coli peptide  deformylase and suggestions on deformylase activities depending  on different metal(II) centres.
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.
Yen
Ngo Thi Hai
NT
Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Greifswald, Germany.
Bogdanović
Xenia
X
Palm
Gottfried J
GJ
Kühl
Olaf
O
Hinrichs
Winfried
W
D000581:Amidohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004789:Enzyme Activation; D004926:Escherichia coli / Q000201:enzymology*; D007501:Iron / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D015032:Zinc / Q000737:chemistry* / Q000378:metabolism
D008024:Ligands; D009532:Nickel; D007501:Iron; D000581:Amidohydrolases; C084507:peptide deformylase; D015032:Zinc