ID   DEF_CYTH3               Reviewed;         184 AA.
AC   Q11X86;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-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=CHU_0693;
OS   Cytophaga hutchinsonii (strain ATCC 33406 / DSM 1761 / CIP 103989 / NBRC
OS   15051 / NCIMB 9469 / D465).
OC   Bacteria; Bacteroidetes; Cytophagia; Cytophagales; Cytophagaceae;
OC   Cytophaga.
OX   NCBI_TaxID=269798;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 33406 / DSM 1761 / CIP 103989 / NBRC 15051 / NCIMB 9469 / D465;
RX   PubMed=17400776; DOI=10.1128/aem.00225-07;
RA   Xie G., Bruce D.C., Challacombe J.F., Chertkov O., Detter J.C., Gilna P.,
RA   Han C.S., Lucas S., Misra M., Myers G.L., Richardson P., Tapia R.,
RA   Thayer N., Thompson L.S., Brettin T.S., Henrissat B., Wilson D.B.,
RA   McBride M.J.;
RT   "Genome sequence of the cellulolytic gliding bacterium Cytophaga
RT   hutchinsonii.";
RL   Appl. Environ. Microbiol. 73:3536-3546(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; CP000383; ABG57980.1; -; Genomic_DNA.
DR   RefSeq; WP_011584096.1; NZ_FPJX01000001.1.
DR   AlphaFoldDB; Q11X86; -.
DR   SMR; Q11X86; -.
DR   STRING; 269798.CHU_0693; -.
DR   EnsemblBacteria; ABG57980; ABG57980; CHU_0693.
DR   KEGG; chu:CHU_0693; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_0_10; -.
DR   OMA; VCIQHEI; -.
DR   OrthoDB; 1649129at2; -.
DR   Proteomes; UP000001822; 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_0000301022"
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   184 AA;  21083 MW;  D466CDF239285D4E CRC64;
     MIYPIVAYGD PVLKKVAQDI EKGSLDVVKM SADMFETMEN AHGVGLAAPQ VALNLRMFVI
     DTSVFDDEKI TPVRKTFINP VIEEEWGDEW PYEEGCLSIP GVRADVYRPA NLRIRYFDTD
     WKEHVEEFDG MTARVIQHEY DHIEGVLFVD HLSSIKKRLL KGKLTNISKG DCDASYRMKF
     PIKK