ID   DEF_RHOP2               Reviewed;         175 AA.
AC   Q2J2C6;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   07-MAR-2006, sequence version 1.
DT   03-AUG-2022, entry version 88.
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=RPB_0673;
OS   Rhodopseudomonas palustris (strain HaA2).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Rhodopseudomonas.
OX   NCBI_TaxID=316058;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HaA2;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA   Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Pelletier D.A.,
RA   Kyrpides N., Anderson I., Oda Y., Harwood C.S., Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris HaA2.";
RL   Submitted (JAN-2006) to the EMBL/GenBank/DDBJ databases.
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; CP000250; ABD05384.1; -; Genomic_DNA.
DR   RefSeq; WP_011439574.1; NC_007778.1.
DR   AlphaFoldDB; Q2J2C6; -.
DR   SMR; Q2J2C6; -.
DR   STRING; 316058.RPB_0673; -.
DR   EnsemblBacteria; ABD05384; ABD05384; RPB_0673.
DR   KEGG; rpb:RPB_0673; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_0_5; -.
DR   OMA; VCIQHEI; -.
DR   OrthoDB; 1649129at2; -.
DR   Proteomes; UP000008809; 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.
FT   CHAIN           1..175
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000301090"
FT   ACT_SITE        139
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         96
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         138
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         142
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ   SEQUENCE   175 AA;  19741 MW;  7F525920823468D3 CRC64;
     MALREIIILP DKRLREISKP VAEVTPEIRK LADDMFESMY EAPGIGLAAI QIAEPVRLIT
     MDIVRKEGNG KSDPRAFINP EIVGASAELN VYEEGCLSIP EYYAEVERPK TVRIRYTDLD
     GQVKEEDADG LFATCIQHEI DHLNGVLFVD HISKLKKAMV VRKFEKAAKR GIKYV