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Literature summary for 3.5.1.88 extracted from

  • Fell, J.; Steele, D.; Hatcher, T.I.; Gherman, B.
    Electronic effects on the reaction mechanism of the metalloenzyme peptide deformylase (2015), Theoret. Chem. Accounts, 134, 71 .
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KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
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 additional information reaction kinetics and thermodynamics, modeling, overview Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ required, catalytic metal ion, bound by Cys90, His132, and His136, metalloenzyme. Fe2+ leads to the lowest activation barriers for nucleophilic attack due to the ability of Fe2+ to act as a Lewis acid and thereby to more strongly coordinate to and activate the substrate carbonyl leading to a decrease in the energy barrier for the reaction. Fe2+ function analysis by using heteroscorpionate N2Sthiolate biomimetic ligand (L) complexed to Fe2+. The high-spin state for the Fe2+-L coordination complexes here has been shown to be the ground state. Reaction of Fe2+-L with formamide leading to formation of Fe2+-L-(formate) and ammonia Escherichia coli
additional information preference for Fe2+ as the active site metal ion, versus, for example, Zn2+, Co2+, or N2+, despite Fe2+ being uncommon for this class of metalloenzymes and that PDF catalyzes a non-redox reaction. The difference in computed activation energies for deformylation between Fe2+, Co2+, and Zn2+ complexes with ligand L is fully consistent with experimental kinetics data for the Fe2+, Co2+, and Zn2+ forms of PDF as well as with the results from the earlier QM/MM computational studies Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A6K3
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Synonyms

Synonyms Comment Organism
PDF
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 Escherichia coli

General Information

General Information Comment Organism
additional information proposed mechanism for the N-terminal deformylation reaction catalyzed by PDF, with active site residues, overview. The catallytic triad is formed by Cys90, His132, and His136. Aanalysis of activation and reaction free energies for deformylation Escherichia coli
physiological function the metalloenzyme peptide deformylase (PDF) plays a crucial role in the biosynthesis of proteins by eubacteria, making the enzyme a promising target for antibacterial agents. In a reaction catalyzed by an Fe2+ coordination complex in the enzyme active site, PDF cleaves a formyl group from the N-terminus of nascent eubacterial proteins Escherichia coli