ID   DEF_BRASO               Reviewed;         175 AA.
AC   A4YLB9;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   03-AUG-2022, entry version 74.
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=BRADO0770;
OS   Bradyrhizobium sp. (strain ORS 278).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Bradyrhizobium; unclassified Bradyrhizobium.
OX   NCBI_TaxID=114615;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ORS 278;
RX   PubMed=17540897; DOI=10.1126/science.1139548;
RA   Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.-C.,
RA   Jaubert M., Simon D., Cartieaux F., Prin Y., Bena G., Hannibal L.,
RA   Fardoux J., Kojadinovic M., Vuillet L., Lajus A., Cruveiller S., Rouy Z.,
RA   Mangenot S., Segurens B., Dossat C., Franck W.L., Chang W.-S., Saunders E.,
RA   Bruce D., Richardson P., Normand P., Dreyfus B., Pignol D., Stacey G.,
RA   Emerich D., Vermeglio A., Medigue C., Sadowsky M.;
RT   "Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia.";
RL   Science 316:1307-1312(2007).
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; CU234118; CAL74695.1; -; Genomic_DNA.
DR   RefSeq; WP_011923950.1; NC_009445.1.
DR   AlphaFoldDB; A4YLB9; -.
DR   SMR; A4YLB9; -.
DR   STRING; 114615.BRADO0770; -.
DR   EnsemblBacteria; CAL74695; CAL74695; BRADO0770.
DR   KEGG; bra:BRADO0770; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_0_5; -.
DR   OMA; VCIQHEI; -.
DR   OrthoDB; 1649129at2; -.
DR   BioCyc; BSP114615:BRADO_RS03620-MON; -.
DR   Proteomes; UP000001994; 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..175
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000301013"
FT   ACT_SITE        141
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         98
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         140
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         144
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ   SEQUENCE   175 AA;  19976 MW;  49B0C8291E41D5C7 CRC64;
     MSLREIIILP DRQLRLVSKP VEKVTPEIRQ LVDDMFQTMY DAPGIGLAAI QVAQPLRVIT
     MDLAKPDSGG ETKREPRVFI NPEIIAKSDE LSVYEEGCLS IPEYYEEVER PARVRVRFTD
     LDGVVREEDA EGLYATCIQH EIDHLNGVLF IDYLSKLKRD RVMKKFTKAA KRAGE