ID   DEF_ENT38               Reviewed;         169 AA.
AC   A4WF95;
DT   05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   27-MAR-2024, entry version 94.
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};
GN   OrderedLocusNames=Ent638_3718;
OS   Enterobacter sp. (strain 638).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Enterobacter.
OX   NCBI_TaxID=399742;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=638;
RX   PubMed=20485560; DOI=10.1371/journal.pgen.1000943;
RA   Taghavi S., van der Lelie D., Hoffman A., Zhang Y.B., Walla M.D.,
RA   Vangronsveld J., Newman L., Monchy S.;
RT   "Genome sequence of the plant growth promoting endophytic bacterium
RT   Enterobacter sp. 638.";
RL   PLoS Genet. 6:E1000943-E1000943(2010).
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}.
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DR   EMBL; CP000653; ABP62375.1; -; Genomic_DNA.
DR   RefSeq; WP_015960696.1; NC_009436.1.
DR   AlphaFoldDB; A4WF95; -.
DR   SMR; A4WF95; -.
DR   STRING; 399742.Ent638_3718; -.
DR   KEGG; ent:Ent638_3718; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_1_6; -.
DR   OrthoDB; 9804313at2; -.
DR   Proteomes; UP000000230; 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:SF21; 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   3: Inferred from homology;
KW   Hydrolase; Iron; Metal-binding; Protein biosynthesis.
FT   CHAIN           1..169
FT                   /note="Peptide deformylase"
FT                   /id="PRO_1000058243"
FT   ACT_SITE        134
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         91
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         133
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         137
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ   SEQUENCE   169 AA;  19403 MW;  4BA3B530A9A6CA26 CRC64;
     MAVLQVLHIP DERLRIVAEP VKEVNAEIQR IVDDMFDTMY AEEGIGLAAT QVDIHKRIIV
     IDVSENREER LVLINPELLE QSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKSFE
     LEADDLLAIC IQHEMDHLVG KLFIDYLSPL KQQRIRQKVE KLDRMRTRA
//