ID   DEF_OPITP               Reviewed;         192 AA.
AC   B1ZMD5;
DT   24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-MAY-2008, sequence version 1.
DT   27-MAR-2024, entry version 78.
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=Oter_0097;
OS   Opitutus terrae (strain DSM 11246 / JCM 15787 / PB90-1).
OC   Bacteria; Verrucomicrobiota; Opitutae; Opitutales; Opitutaceae; Opitutus.
OX   NCBI_TaxID=452637;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 11246 / JCM 15787 / PB90-1;
RX   PubMed=21398538; DOI=10.1128/jb.00228-11;
RA   van Passel M.W., Kant R., Palva A., Copeland A., Lucas S., Lapidus A.,
RA   Glavina del Rio T., Pitluck S., Goltsman E., Clum A., Sun H., Schmutz J.,
RA   Larimer F.W., Land M.L., Hauser L., Kyrpides N., Mikhailova N.,
RA   Richardson P.P., Janssen P.H., de Vos W.M., Smidt H.;
RT   "Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an
RT   abundant inhabitant of rice paddy soil ecosystems.";
RL   J. Bacteriol. 193:2367-2368(2011).
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; CP001032; ACB73388.1; -; Genomic_DNA.
DR   RefSeq; WP_012372926.1; NC_010571.1.
DR   AlphaFoldDB; B1ZMD5; -.
DR   SMR; B1ZMD5; -.
DR   STRING; 452637.Oter_0097; -.
DR   KEGG; ote:Oter_0097; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_4_2_0; -.
DR   OrthoDB; 9784988at2; -.
DR   Proteomes; UP000007013; 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:SF22; 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; Reference proteome.
FT   CHAIN           1..192
FT                   /note="Peptide deformylase"
FT                   /id="PRO_1000097328"
FT   ACT_SITE        151
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         108
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         150
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"
SQ   SEQUENCE   192 AA;  21428 MW;  49327B8C522408E3 CRC64;
     MSLRIVHYND PVLRRKGEKI TAFDKALSQL AKEMLATMQE AAGIGLAAQQ IGRPVQLCVV
     DLRRAEIDFT WELDGAKPPL DLIMPMIITN PEITPDRETD VYLVEEGCLS FPKIRGDVPR
     PDAITVRYQD EHGTPHTLHC DGLLARCIQH EVDHLNGVLF IDRMEKKTRA AIDADVKTLA
     KITRAAAKLN PA
//