ID   DEF_LACJO               Reviewed;         184 AA.
AC   Q74JW2;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 111.
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=LJ_0993;
OS   Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533).
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
OC   Lactobacillus.
OX   NCBI_TaxID=257314;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CNCM I-1225 / La1 / NCC 533;
RX   PubMed=14983040; DOI=10.1073/pnas.0307327101;
RA   Pridmore R.D., Berger B., Desiere F., Vilanova D., Barretto C.,
RA   Pittet A.-C., Zwahlen M.-C., Rouvet M., Altermann E., Barrangou R.,
RA   Mollet B., Mercenier A., Klaenhammer T., Arigoni F., Schell M.A.;
RT   "The genome sequence of the probiotic intestinal bacterium Lactobacillus
RT   johnsonii NCC 533.";
RL   Proc. Natl. Acad. Sci. U.S.A. 101:2512-2517(2004).
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;
CC         Evidence={ECO:0000255|HAMAP-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; AE017198; AAS08815.1; -; Genomic_DNA.
DR   RefSeq; WP_004894291.1; NC_005362.1.
DR   AlphaFoldDB; Q74JW2; -.
DR   SMR; Q74JW2; -.
DR   STRING; 257314.LJ_0993; -.
DR   EnsemblBacteria; AAS08815; AAS08815; LJ_0993.
DR   GeneID; 66435591; -.
DR   KEGG; ljo:LJ_0993; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_4_0_9; -.
DR   OMA; DMMEYLV; -.
DR   Proteomes; UP000000581; 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; -; 1.
DR   HAMAP; MF_00163; Pep_deformylase; 1.
DR   InterPro; IPR023635; Peptide_deformylase.
DR   InterPro; IPR036821; Peptide_deformylase_sf.
DR   PANTHER; PTHR10458; PTHR10458; 1.
DR   Pfam; PF01327; Pep_deformylase; 1.
DR   PIRSF; PIRSF004749; Pep_def; 1.
DR   PRINTS; PR01576; PDEFORMYLASE.
DR   SUPFAM; SSF56420; SSF56420; 1.
DR   TIGRFAMs; TIGR00079; pept_deformyl; 1.
PE   3: Inferred from homology;
KW   Hydrolase; Iron; Metal-binding; Protein biosynthesis; Reference proteome.
FT   CHAIN           1..184
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000301047"
FT   ACT_SITE        155
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         111
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         154
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         158
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ   SEQUENCE   184 AA;  20791 MW;  43DDA10729328290 CRC64;
     MILMHDITRD GNPVLRQVAK PLTFPLSDEY KKLADDMMQY LINSQDPKIA EKHQLRAGVG
     LAAPQVGESV QMAALLVPND KGEIIFKEVF VNPKILSESV RRTCLAEGEG CLSVDKDIEG
     YVPRPDKLKI RYYTVDGEEK TIRLKDYPAI VASHEIDHLN GHLFYDRINK QNPFELAEDT
     IVIS