ID   DEF_SYMTH               Reviewed;         217 AA.
AC   Q67PR5;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2004, sequence version 1.
DT   02-SEP-2026, entry version 115.
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=STH1343;
OS   Symbiobacterium thermophilum (strain DSM 24528 / JCM 14929 / IAM 14863 /
OS   T).
OC   Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales;
OC   Symbiobacteriaceae; Symbiobacterium.
OX   NCBI_TaxID=292459;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 24528 / JCM 14929 / IAM 14863 / T;
RX   PubMed=15383646; DOI=10.1093/nar/gkh830;
RA   Ueda K., Yamashita A., Ishikawa J., Shimada M., Watsuji T., Morimura K.,
RA   Ikeda H., Hattori M., Beppu T.;
RT   "Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium
RT   that depends on microbial commensalism.";
RL   Nucleic Acids Res. 32:4937-4944(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=N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal
CC         L-methionyl-[peptide] + formate; 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; AP006840; BAD40328.1; -; Genomic_DNA.
DR   RefSeq; WP_011195474.1; NC_006177.1.
DR   AlphaFoldDB; Q67PR5; -.
DR   SMR; Q67PR5; -.
DR   STRING; 292459.STH1343; -.
DR   KEGG; sth:STH1343; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_4_2_9; -.
DR   OrthoDB; 9784988at2; -.
DR   Proteomes; UP000000417; Chromosome.
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   FunFam; 3.90.45.10:FF:000005; Peptide 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   NCBIfam; NF001159; PRK00150.1-3; 1.
DR   PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1.
DR   PANTHER; PTHR10458:SF22; PEPTIDE DEFORMYLASE; 1.
DR   Pfam; PF01327; Pep_deformylase; 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..217
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000301114"
FT   REGION          153..217
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        155..176
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        177..192
FT                   /note="Low complexity"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        206..217
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        134
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         91
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         133
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT   BINDING         137
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ   SEQUENCE   217 AA;  23242 MW;  DAA0BEF5C915026C CRC64;
     MAILEIVKEP AEVLRKKAKP VTKINASIRK LLDDMTETMY AAPGVGLAAP QVGVSKRLIV
     VDPQDGSGQL YQLINPEIVK AEGWVKGTEG CLSIPGMVGD VWRYEKVQVV ALDRTGKKVW
     IDAEGYLARI FQHEIDHLDG ILYTDKCTNL RPVSEDGEEE EEAEVAEVMP EPEAEGAGEP
     SAEGAGQAAA EAGAEEGEQV TTGVSGERRG SAAAKEE
//