DEF_ECOLI
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 03-AUG-2022, entry version 145.
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; Proteobacteria; 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 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; P0A6K3; -.
DR PRIDE; P0A6K3; -.
DR EnsemblBacteria; AAC76312; AAC76312; b3287.
DR EnsemblBacteria; BAE78005; BAE78005; BAE78005.
DR GeneID; 67415327; -.
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 PhylomeDB; P0A6K3; -.
DR BioCyc; EcoCyc:EG11440-MON; -.
DR BioCyc; MetaCyc:EG11440-MON; -.
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; IBA:GO_Central.
DR GO; GO:0031365; P:N-terminal protein amino acid modification; IDA:EcoliWiki.
DR GO; GO:0018206; P:peptidyl-methionine modification; IBA:GO_Central.
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 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
