ID   DEF_ECOLI               Reviewed;         169 AA.
AC   P0A6K3; P27251; Q2M6V1;
DT   29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   24-JAN-2024, entry version 153.
DE   RecName: Full=Peptide deformylase;
DE            Short=PDF;
DE            EC=3.5.1.88 {ECO:0000269|PubMed:7896716};
DE   AltName: Full=Polypeptide deformylase;
GN   Name=def; Synonyms=fms {ECO:0000303|PubMed:8244948};
GN   OrderedLocusNames=b3287, JW3248;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC   STRAIN=K12;
RX   PubMed=8112305; DOI=10.1002/j.1460-2075.1994.tb06335.x;
RA   Mazel D., Pochet S., Marliere P.;
RT   "Genetic characterization of polypeptide deformylase, a distinctive enzyme
RT   of eubacterial translation.";
RL   EMBO J. 13:914-923(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12 / K37;
RX   PubMed=1624424; DOI=10.1128/jb.174.13.4294-4301.1992;
RA   Guillon J.-M., Mechulam Y., Schmitter J.-M., Blanquet S., Fayat G.;
RT   "Disruption of the gene for Met-tRNA(fMet) formyltransferase severely
RT   impairs growth of Escherichia coli.";
RL   J. Bacteriol. 174:4294-4301(1992).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16.
RC   STRAIN=K12 / K37;
RX   PubMed=8432722; DOI=10.1128/jb.175.4.993-1000.1993;
RA   Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S.;
RT   "The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet)
RT   formyltransferase, escapes metabolic control.";
RL   J. Bacteriol. 175:993-1000(1993).
RN   [6]
RP   PROTEIN SEQUENCE OF 2-7, COFACTOR, AND MASS SPECTROMETRY.
RX   PubMed=8244948; DOI=10.1128/jb.175.23.7737-7740.1993;
RA   Meinnel T., Blanquet S.;
RT   "Evidence that peptide deformylase and methionyl-tRNA(fMet)
RT   formyltransferase are encoded within the same operon in Escherichia coli.";
RL   J. Bacteriol. 175:7737-7740(1993).
RN   [7]
RP   FUNCTION, ACTIVITY REGULATION, COFACTOR, AND CATALYTIC ACTIVITY.
RX   PubMed=7896716; DOI=10.1128/jb.177.7.1883-1887.1995;
RA   Meinnel T., Blanquet S.;
RT   "Enzymatic properties of Escherichia coli peptide deformylase.";
RL   J. Bacteriol. 177:1883-1887(1995).
RN   [8]
RP   COFACTOR.
RX   PubMed=9610360; DOI=10.1006/bbrc.1998.8616;
RA   Groche D., Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.;
RT   "Isolation and crystallization of functionally competent Escherichia coli
RT   peptide deformylase forms containing either iron or nickel in the active
RT   site.";
RL   Biochem. Biophys. Res. Commun. 246:342-346(1998).
RN   [9]
RP   STRUCTURE BY NMR.
RX   PubMed=8845003; DOI=10.1006/jmbi.1996.0521;
RA   Meinnel T., Blanquet S., Dardel F.;
RT   "A new subclass of the zinc metalloproteases superfamily revealed by the
RT   solution structure of peptide deformylase.";
RL   J. Mol. Biol. 262:375-386(1996).
RN   [10]
RP   STRUCTURE BY NMR.
RX   PubMed=9665852; DOI=10.1006/jmbi.1998.1882;
RA   Dardel F., Ragusa S., Lazennec C., Blanquet S., Meinnel T.;
RT   "Solution structure of nickel-peptide deformylase.";
RL   J. Mol. Biol. 280:501-513(1998).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
RX   PubMed=9374869; DOI=10.1021/bi9711543;
RA   Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.;
RT   "Crystal structure of the Escherichia coli peptide deformylase.";
RL   Biochemistry 36:13904-13909(1997).
RN   [12]
RP   ERRATUM OF PUBMED:9374869.
RA   Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.;
RL   Biochemistry 37:13042-13042(1998).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX   PubMed=9565550; DOI=10.1074/jbc.273.19.11413;
RA   Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.;
RT   "Structure of peptide deformylase and identification of the substrate
RT   binding site.";
RL   J. Biol. Chem. 273:11413-11416(1998).
RN   [14]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH IRON, COFACTOR, AND
RP   ACTIVE SITE.
RX   PubMed=9846875; DOI=10.1038/4162;
RA   Becker A., Schlichting I., Kabsch W., Groche D., Schultz S., Wagner A.F.;
RT   "Iron center, substrate recognition and mechanism of peptide deformylase.";
RL   Nat. Struct. Biol. 5:1053-1058(1998).
RN   [15]
RP   X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 2-169.
RX   PubMed=10200158; DOI=10.1021/bi982594c;
RA   Hao B., Gong W., Rajagopalan P.T.R., Zhou Y., Pei D., Chan M.K.;
RT   "Structural basis for the design of antibiotics targeting peptide
RT   deformylase.";
RL   Biochemistry 38:4712-4719(1999).
CC   -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC       synthesized proteins (PubMed:7896716). Requires at least a dipeptide
CC       for an efficient rate of reaction. N-terminal L-methionine is a
CC       prerequisite for activity but the enzyme has broad specificity at other
CC       positions. {ECO:0000269|PubMed:7896716, ECO:0000269|PubMed:9610360,
CC       ECO:0000305|PubMed:8244948}.
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:0000269|PubMed:7896716};
CC       PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:24422;
CC         Evidence={ECO:0000305|PubMed:7896716};
CC   -!- COFACTOR:
CC       Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC         Evidence={ECO:0000269|PubMed:9610360, ECO:0000269|PubMed:9846875};
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000269|PubMed:8244948, ECO:0000305|PubMed:7896716};
CC       Note=Upon overproduction is isolated with 1 Fe(2+) ion per monomer, a
CC       Ni(2+)-bound form is as active while a Zn(2+)-bound form is inactive
CC       (PubMed:9610360). {ECO:0000269|PubMed:9610360};
CC   -!- ACTIVITY REGULATION: Inhibited by 1,10-phenanthroline.
CC       {ECO:0000269|PubMed:7896716}.
CC   -!- SUBUNIT: Monomer.
CC   -!- INTERACTION:
CC       P0A6K3; P60723: rplD; NbExp=4; IntAct=EBI-548913, EBI-545597;
CC       P0A6K3; P0AG44: rplQ; NbExp=3; IntAct=EBI-548913, EBI-544558;
CC       P0A6K3; P61175: rplV; NbExp=3; IntAct=EBI-548913, EBI-542255;
CC       P0A6K3; P08390: usg; NbExp=3; IntAct=EBI-548913, EBI-548921;
CC   -!- MASS SPECTROMETRY: Mass=19175; Mass_error=50; Method=MALDI;
CC       Evidence={ECO:0000269|PubMed:8244948};
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
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DR   EMBL; X77800; CAA54826.1; -; Genomic_DNA.
DR   EMBL; X63666; CAA45206.1; -; Genomic_DNA.
DR   EMBL; X65946; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; X77091; CAA54367.1; -; Genomic_DNA.
DR   EMBL; U18997; AAA58084.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76312.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE78005.1; -; Genomic_DNA.
DR   PIR; S23107; S23107.
DR   RefSeq; NP_417745.1; NC_000913.3.
DR   RefSeq; WP_000114984.1; NZ_STEB01000038.1.
DR   PDB; 1BS4; X-ray; 1.90 A; A/B/C=2-169.
DR   PDB; 1BS5; X-ray; 2.50 A; A/B/C=2-169.
DR   PDB; 1BS6; X-ray; 2.10 A; A/B/C=2-169.
DR   PDB; 1BS7; X-ray; 2.50 A; A/B/C=2-169.
DR   PDB; 1BS8; X-ray; 2.20 A; A/B/C=2-169.
DR   PDB; 1BSJ; X-ray; 3.00 A; A=2-169.
DR   PDB; 1BSK; X-ray; 3.00 A; A=2-169.
DR   PDB; 1BSZ; X-ray; 1.90 A; A/B/C=2-169.
DR   PDB; 1DEF; NMR; -; A=2-148.
DR   PDB; 1DFF; X-ray; 2.88 A; A=2-165.
DR   PDB; 1G27; X-ray; 2.10 A; A/B/C=2-169.
DR   PDB; 1G2A; X-ray; 1.75 A; A/B/C=2-169.
DR   PDB; 1ICJ; X-ray; 1.90 A; A/B/C=2-169.
DR   PDB; 1LRU; X-ray; 2.10 A; A/B/C=2-169.
DR   PDB; 1XEM; X-ray; 1.76 A; A=2-169.
DR   PDB; 1XEN; X-ray; 1.85 A; A=2-169.
DR   PDB; 1XEO; X-ray; 1.30 A; A=2-169.
DR   PDB; 2AI8; X-ray; 1.70 A; A/B/C=2-169.
DR   PDB; 2DEF; NMR; -; A=3-148.
DR   PDB; 2KMN; NMR; -; A=2-148.
DR   PDB; 2W3T; X-ray; 1.69 A; A=2-169.
DR   PDB; 2W3U; X-ray; 1.96 A; A=2-169.
DR   PDB; 3K6L; X-ray; 2.15 A; A/B/C=1-169.
DR   PDB; 4AL2; X-ray; 2.60 A; A/B/C=2-169.
DR   PDB; 4AL3; X-ray; 1.98 A; A=2-169.
DR   PDB; 4AZ4; X-ray; 1.80 A; A=2-169.
DR   PDB; 4V5B; X-ray; 3.74 A; A5=147-162.
DR   PDB; 6IY7; EM; 10.50 A; P=1-169.
DR   PDB; 6IZI; EM; 11.80 A; P=1-169.
DR   PDB; 7D6Z; EM; 3.40 A; g=1-169.
DR   PDB; 7D80; EM; 4.10 A; 3=1-169.
DR   PDBsum; 1BS4; -.
DR   PDBsum; 1BS5; -.
DR   PDBsum; 1BS6; -.
DR   PDBsum; 1BS7; -.
DR   PDBsum; 1BS8; -.
DR   PDBsum; 1BSJ; -.
DR   PDBsum; 1BSK; -.
DR   PDBsum; 1BSZ; -.
DR   PDBsum; 1DEF; -.
DR   PDBsum; 1DFF; -.
DR   PDBsum; 1G27; -.
DR   PDBsum; 1G2A; -.
DR   PDBsum; 1ICJ; -.
DR   PDBsum; 1LRU; -.
DR   PDBsum; 1XEM; -.
DR   PDBsum; 1XEN; -.
DR   PDBsum; 1XEO; -.
DR   PDBsum; 2AI8; -.
DR   PDBsum; 2DEF; -.
DR   PDBsum; 2KMN; -.
DR   PDBsum; 2W3T; -.
DR   PDBsum; 2W3U; -.
DR   PDBsum; 3K6L; -.
DR   PDBsum; 4AL2; -.
DR   PDBsum; 4AL3; -.
DR   PDBsum; 4AZ4; -.
DR   PDBsum; 4V5B; -.
DR   PDBsum; 6IY7; -.
DR   PDBsum; 6IZI; -.
DR   PDBsum; 7D6Z; -.
DR   PDBsum; 7D80; -.
DR   AlphaFoldDB; P0A6K3; -.
DR   EMDB; EMD-30598; -.
DR   EMDB; EMD-30611; -.
DR   EMDB; EMD-9750; -.
DR   EMDB; EMD-9753; -.
DR   SMR; P0A6K3; -.
DR   BioGRID; 4263416; 59.
DR   BioGRID; 852092; 4.
DR   DIP; DIP-47953N; -.
DR   IntAct; P0A6K3; 63.
DR   STRING; 511145.b3287; -.
DR   BindingDB; P0A6K3; -.
DR   DrugBank; DB02276; (S)-2-(Phosphonoxy)Caproyl-L-Leucyl-P-Nitroanilide.
DR   DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR   DrugBank; DB08523; [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL.
DR   DrugBank; DB04368; Bb-3497.
DR   DrugBank; DB01942; Formic acid.
DR   jPOST; P0A6K3; -.
DR   PaxDb; 511145-b3287; -.
DR   EnsemblBacteria; AAC76312; AAC76312; b3287.
DR   GeneID; 83578256; -.
DR   GeneID; 947780; -.
DR   KEGG; ecj:JW3248; -.
DR   KEGG; eco:b3287; -.
DR   PATRIC; fig|1411691.4.peg.3445; -.
DR   EchoBASE; EB1410; -.
DR   eggNOG; COG0242; Bacteria.
DR   HOGENOM; CLU_061901_2_1_6; -.
DR   InParanoid; P0A6K3; -.
DR   OMA; VCIQHEI; -.
DR   OrthoDB; 9804313at2; -.
DR   PhylomeDB; P0A6K3; -.
DR   BioCyc; EcoCyc:EG11440-MONOMER; -.
DR   BioCyc; MetaCyc:EG11440-MONOMER; -.
DR   BRENDA; 3.5.1.88; 2026.
DR   SABIO-RK; P0A6K3; -.
DR   EvolutionaryTrace; P0A6K3; -.
DR   PRO; PR:P0A6K3; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0008198; F:ferrous iron binding; IDA:EcoCyc.
DR   GO; GO:0016787; F:hydrolase activity; IDA:EcoliWiki.
DR   GO; GO:0042586; F:peptide deformylase activity; IDA:EcoliWiki.
DR   GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR   GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
DR   GO; GO:0043686; P:co-translational protein modification; IPI:EcoCyc.
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:SF21; 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   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; Hydrolase; Iron; Metal-binding;
KW   Protein biosynthesis; Reference proteome; Zinc.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:8244948"
FT   CHAIN           2..169
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000082779"
FT   ACT_SITE        134
FT                   /evidence="ECO:0000269|PubMed:9846875"
FT   BINDING         91
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000269|PubMed:9846875"
FT   BINDING         133
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000269|PubMed:9846875"
FT   BINDING         137
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000269|PubMed:9846875"
FT   HELIX           12..15
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   HELIX           26..41
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   STRAND          45..48
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   HELIX           49..52
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   STRAND          56..61
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   STRAND          65..68
FT                   /evidence="ECO:0007829|PDB:1BS6"
FT   STRAND          71..82
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   STRAND          85..89
FT                   /evidence="ECO:0007829|PDB:2W3T"
FT   STRAND          92..94
FT                   /evidence="ECO:0007829|PDB:1DEF"
FT   STRAND          99..103
FT                   /evidence="ECO:0007829|PDB:2W3T"
FT   STRAND          105..112
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   STRAND          114..116
FT                   /evidence="ECO:0007829|PDB:1DEF"
FT   STRAND          118..123
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   HELIX           125..138
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   HELIX           143..146
FT                   /evidence="ECO:0007829|PDB:1XEO"
FT   HELIX           149..165
FT                   /evidence="ECO:0007829|PDB:1XEO"
SQ   SEQUENCE   169 AA;  19328 MW;  C485EB6C1D2D91B8 CRC64;
     MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV
     IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL VPRAEKVKIR ALDRDGKPFE
     LEADGLLAIC IQHEMDHLVG KLFMDYLSPL KQQRIRQKVE KLDRLKARA
//