ID   DEF_CLOB8               Reviewed;         136 AA.
AC   O08450; A6LZ54;
DT   15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-1997, sequence version 1.
DT   03-AUG-2022, entry version 115.
DE   RecName: Full=Peptide deformylase;
DE            Short=PDF;
DE            EC=3.5.1.88;
DE   AltName: Full=Polypeptide deformylase;
GN   Name=def; Synonyms=fms; OrderedLocusNames=Cbei_3511;
OS   Clostridium beijerinckii (strain ATCC 51743 / NCIMB 8052) (Clostridium
OS   acetobutylicum).
OC   Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC   Clostridium.
OX   NCBI_TaxID=290402;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=9572951; DOI=10.1128/aem.64.5.1780-1785.1998;
RA   Evans V.J., Liyanage H., Ravagnani A., Young M., Kashket E.R.;
RT   "Truncation of peptide deformylase reduces the growth rate and stabilizes
RT   solvent production in Clostridium beijerinckii NCIMB 8052.";
RL   Appl. Environ. Microbiol. 64:1780-1785(1998).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51743 / NCIMB 8052;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Sims D., Brettin T., Bruce D., Tapia R., Brainard J., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Bennet G.,
RA   Cann I., Chen J.-S., Contreras A.L., Jones D., Kashket E., Mitchell W.,
RA   Stoddard S., Schwarz W., Qureshi N., Young M., Shi Z., Ezeji T., White B.,
RA   Blaschek H., Richardson P.;
RT   "Complete sequence of Clostridium beijerinckii NCIMB 8052.";
RL   Submitted (JUN-2007) 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 (By
CC       similarity). {ECO:0000250}.
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   -!- COFACTOR:
CC       Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC       Note=Binds 1 Fe(2+) ion. {ECO:0000250};
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
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DR   EMBL; Z96934; CAB09662.1; -; Genomic_DNA.
DR   EMBL; CP000721; ABR35634.1; -; Genomic_DNA.
DR   RefSeq; WP_012059684.1; NC_009617.1.
DR   AlphaFoldDB; O08450; -.
DR   SMR; O08450; -.
DR   STRING; 290402.Cbei_3511; -.
DR   EnsemblBacteria; ABR35634; ABR35634; Cbei_3511.
DR   KEGG; cbe:Cbei_3511; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_3_1_9; -.
DR   OMA; HEMDHFE; -.
DR   OrthoDB; 1649129at2; -.
DR   Proteomes; UP000000565; 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.
PE   3: Inferred from homology;
KW   Hydrolase; Iron; Metal-binding; Protein biosynthesis.
FT   CHAIN           1..136
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000082768"
FT   ACT_SITE        127
FT                   /evidence="ECO:0000250"
FT   BINDING         85
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         126
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         130
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   136 AA;  15623 MW;  7E9CE063FFDE9BE6 CRC64;
     MIKPIVKDIL FLGQKSEEAT KNDMVVIDDL IDTLRANLEH CVGLAANMIG VKKRILVFTV
     GNLIVPMINP VILKKEKPYE TEESCLSLIG FRKTKRYETI EVTYLDRNFN KKKQVFNGFT
     AQIIQHEMDH FEGIII