IUBMB Enzyme Nomenclature

EC 3.5.1.88

Accepted name: peptide deformylase

Reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide

Systematic name: formyl-L-methionyl peptide amidohydrolase

Comments: Requires Fe(II). Also requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. Differs in substrate specifity from EC 3.5.1.27 (N-formylmethionylaminoacyl-tRNA deformylase) and EC 3.5.1.31 (formylmethionine deformylase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 369636-51-1

References:

1. Adams, J.M. On the release of the formyl group from nascent protein. J. Mol. Biol. 33 (1968) 571-589. [PMID: 4973445]

2. Mazel, D., Pochet, S. and Marliere, P. Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J. 13 (1994) 914-923. [PMID: 8112305]

3. Chan, M.K., Gong, W., Rajagopalan, P.T.R., Hao, B., Tsai, C.M. and Pei, D. Crystal structure of the Escherichia coli peptide deformylase. Biochemistry 36 (1997) 13904-13909. [PMID: 9374869]

4. Becker, A., Schlichting, I., Kabsch, W., Schultz, S. and Wagner, A.F.V. Structure of peptide deformylase and identification of the substrate binding site. J. Biol. Chem. 273 (1998) 11413-11416. [PMID: 9565550]

5. Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S. and Wagner, A.F. Iron center, substrate recognition, and mechanism of peptide deformylase. Nat. Struct. Biol. 5 (1998) 1053-1058. [PMID: 9846875]

6. Rajagopalan, P.T.R., Yu, X.C. and Pei, D. Peptide deformylase: a new type of mononuclear iron protein. J. Am. Chem. Soc. 119 (1997) 12418-12419.

7. Groche, D., Becker, A., Schlichting, I., Kabsch, W., Schultz, S. and Wagner, A.F.V. Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem. Biophys. Res. Commun. 246 (1998) 342-346. [PMID: 9610360]

8. Rajagopalan, P.T.R., Grimme, S. and Pei, D. Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133. Biochemistry 39 (2000) 779-790. [PMID: 10651644]

9. Hu, Y.J., Wei, Y., Zhou, Y., Rajagopalan, P.T.R. and Pei, D. Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library. Biochemistry 38 (1999) 643-650. [PMID: 9888804]

10. Ragasu, S., Mouchet, P., Lazennec, C., Dive, V. and Meinnel, T. Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin. J. Mol. Biol. 289 (1999) 1445-1457. [PMID: 10373378]

11. Giglione, C., Pierre, M. and Meinnel, T. Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents. Mol. Microbiol. 36 (2000) 1197-1205. [PMID: 10931273]

12. Pei, D. Peptide deformylase: a target for novel antibiotics? Emerging Therapeutic Targets 5 (2001) 23-40.

[EC 3.5.1.88 created 2001]


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