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DEF_RHOPS
ID   DEF_RHOPS               Reviewed;         175 AA.
AC   Q13F18;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   31-OCT-2006, sequence version 1.
DT   03-AUG-2022, entry version 86.
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=RPD_0081;
OS   Rhodopseudomonas palustris (strain BisB5).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Rhodopseudomonas.
OX   NCBI_TaxID=316057;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=BisB5;
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   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Pelletier D.A., Kyrpides N., Lykidis A., Oda Y., Harwood C.S.,
RA   Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris BisB5.";
RL   Submitted (MAR-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; CP000283; ABE37321.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q13F18; -.
DR   SMR; Q13F18; -.
DR   STRING; 316057.RPD_0081; -.
DR   EnsemblBacteria; ABE37321; ABE37321; RPD_0081.
DR   KEGG; rpd:RPD_0081; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_0_5; -.
DR   OMA; VCIQHEI; -.
DR   OrthoDB; 1649129at2; -.
DR   BioCyc; RPAL316057:RPD_RS00405-MON; -.
DR   Proteomes; UP000001818; 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_0000301089"
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;  19687 MW;  98C170300FE8832C CRC64;
     MALREIIILP DKRLREISKP VAEVTPEIRK LADDMFESMY DAPGIGLAAI QIAEPVRLIT
     MDIVRKEGNG KSDPRAFINP EIVGASAEMN VYEEGCLSIP EYYADVERPA VVRIRYTDLD
     GNVKEEDADG LFATCIQHEI DHLDGVLFVD HLSKLKRAMV VRKFEKAAKR GIKYV
 
 
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