Iron center, substrate recognition and mechanism of peptide deformylase.
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
Becker
A
A
Max-Planck-Institut für Medizinische Forschung, Abteilung Biophysik, Heidelberg, Germany.
Schlichting
I
I
Kabsch
W
W
Groche
D
D
Schultz
S
S
Wagner
A F
AF
D000581:Amidohydrolases; D000626:Aminopeptidases / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D005296:Ferrous Compounds / Q000378:metabolism; D007501:Iron / Q000737:chemistry; D008667:Metalloproteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009532:Nickel / Q000378:metabolism; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D015032:Zinc / Q000378:metabolism
D005296:Ferrous Compounds; D008667:Metalloproteins; D009532:Nickel; D007501:Iron; D000626:Aminopeptidases; D000581:Amidohydrolases; C084507:peptide deformylase; D015032:Zinc