ID DEF_ENTFA Reviewed; 187 AA. AC Q82ZJ0; DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot. DT 01-JUN-2003, sequence version 1. DT 27-MAR-2024, entry version 109. DE RecName: Full=Peptide deformylase {ECO:0000255|HAMAP-Rule:MF_00163}; DE Short=PDF {ECO:0000255|HAMAP-Rule:MF_00163}; DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163}; DE AltName: Full=Polypeptide deformylase {ECO:0000255|HAMAP-Rule:MF_00163}; GN Name=def {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=EF_3066; OS Enterococcus faecalis (strain ATCC 700802 / V583). OC Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; OC Enterococcus. OX NCBI_TaxID=226185; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 700802 / V583; RX PubMed=12663927; DOI=10.1126/science.1080613; RA Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R., RA Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H., RA Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C., RA DeBoy R.T., Durkin S.A., Kolonay J.F., Madupu R., Nelson W.C., RA Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M., RA Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M.; RT "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus RT faecalis."; RL Science 299:2071-2074(2003). CC -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly CC synthesized proteins. Requires at least a dipeptide for an efficient CC rate of reaction. N-terminal L-methionine is a prerequisite for CC activity but the enzyme has broad specificity at other positions. CC {ECO:0000255|HAMAP-Rule:MF_00163}. CC -!- CATALYTIC ACTIVITY: CC Reaction=H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N- CC terminal L-methionyl-[peptide]; Xref=Rhea:RHEA:24420, Rhea:RHEA- CC COMP:10639, Rhea:RHEA-COMP:10640, ChEBI:CHEBI:15377, CC ChEBI:CHEBI:15740, ChEBI:CHEBI:49298, ChEBI:CHEBI:64731; EC=3.5.1.88; CC Evidence={ECO:0000255|HAMAP-Rule:MF_00163}; CC -!- COFACTOR: CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00163}; CC Note=Binds 1 Fe(2+) ion. {ECO:0000255|HAMAP-Rule:MF_00163}; CC -!- SIMILARITY: Belongs to the polypeptide deformylase family. CC {ECO:0000255|HAMAP-Rule:MF_00163}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE016830; AAO82748.1; -; Genomic_DNA. DR RefSeq; NP_816678.1; NC_004668.1. DR RefSeq; WP_002354981.1; NZ_KE136524.1. DR PDB; 2OS0; X-ray; 1.30 A; A=1-187. DR PDB; 2OS1; X-ray; 1.50 A; A=1-187. DR PDBsum; 2OS0; -. DR PDBsum; 2OS1; -. DR AlphaFoldDB; Q82ZJ0; -. DR SMR; Q82ZJ0; -. DR STRING; 226185.EF_3066; -. DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide. DR EnsemblBacteria; AAO82748; AAO82748; EF_3066. DR GeneID; 60894955; -. DR KEGG; efa:EF3066; -. DR PATRIC; fig|226185.45.peg.505; -. DR eggNOG; COG0242; Bacteria. DR HOGENOM; CLU_061901_4_0_9; -. DR EvolutionaryTrace; Q82ZJ0; -. DR Proteomes; UP000001415; Chromosome. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0042586; F:peptide deformylase activity; IEA:UniProtKB-UniRule. DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule. DR CDD; cd00487; Pep_deformylase; 1. DR Gene3D; 3.90.45.10; Peptide deformylase; 1. DR HAMAP; MF_00163; Pep_deformylase; 1. DR InterPro; IPR023635; Peptide_deformylase. DR InterPro; IPR036821; Peptide_deformylase_sf. DR NCBIfam; TIGR00079; pept_deformyl; 1. DR PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1. DR PANTHER; PTHR10458:SF8; PEPTIDE DEFORMYLASE; 1. DR Pfam; PF01327; Pep_deformylase; 1. DR PIRSF; PIRSF004749; Pep_def; 1. DR PRINTS; PR01576; PDEFORMYLASE. DR SUPFAM; SSF56420; Peptide deformylase; 1. PE 1: Evidence at protein level; KW 3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis; KW Reference proteome. FT CHAIN 1..187 FT /note="Peptide deformylase" FT /id="PRO_0000082782" FT ACT_SITE 158 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 114 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 157 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 161 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT HELIX 4..6 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 13..16 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 28..45 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 47..53 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 59..62 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 63..66 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 70..77 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 89..101 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 105..108 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 127..136 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 142..148 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 149..162 FT /evidence="ECO:0007829|PDB:2OS0" FT HELIX 167..170 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 173..175 FT /evidence="ECO:0007829|PDB:2OS0" FT STRAND 184..186 FT /evidence="ECO:0007829|PDB:2OS0" SQ SEQUENCE 187 AA; 20912 MW; 9CAF46335311B0B2 CRC64; MITMKDIIRE GNPTLRAVAE EVPVPITEED RQLGEDMLTF LKNSQDPVKA EELQLRGGVG LAAPQLDISK RIIAVHVPSN DPENETPSLS TVMYNPKILS HSVQDVCLGE GEGCLSVDRD VPGYVVRHNK ITVSYFDMAG EKHKVRLKNY EAIVVQHEID HINGIMFYDH INKENPFALK EGVLVIE //