DEF_ENTFA
ID DEF_ENTFA Reviewed; 187 AA.
AC Q82ZJ0;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=EF_3066;
OS Enterococcus faecalis (strain ATCC 700802 / V583).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
OC Enterococcus.
OX NCBI_TaxID=226185;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700802 / V583;
RX PubMed=12663927; DOI=10.1126/science.1080613;
RA Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R.,
RA Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H.,
RA Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C.,
RA DeBoy R.T., Durkin S.A., Kolonay J.F., Madupu R., Nelson W.C.,
RA Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M.,
RA Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M.;
RT "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus
RT faecalis.";
RL Science 299:2071-2074(2003).
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; AE016830; AAO82748.1; -; Genomic_DNA.
DR RefSeq; NP_816678.1; NC_004668.1.
DR RefSeq; WP_002354981.1; NZ_KE136524.1.
DR PDB; 2OS0; X-ray; 1.30 A; A=1-187.
DR PDB; 2OS1; X-ray; 1.50 A; A=1-187.
DR PDBsum; 2OS0; -.
DR PDBsum; 2OS1; -.
DR AlphaFoldDB; Q82ZJ0; -.
DR SMR; Q82ZJ0; -.
DR STRING; 226185.EF_3066; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR EnsemblBacteria; AAO82748; AAO82748; EF_3066.
DR GeneID; 60894955; -.
DR KEGG; efa:EF3066; -.
DR PATRIC; fig|226185.45.peg.505; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR EvolutionaryTrace; Q82ZJ0; -.
DR Proteomes; UP000001415; 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 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis;
KW Reference proteome.
FT CHAIN 1..187
FT /note="Peptide deformylase"
FT /id="PRO_0000082782"
FT ACT_SITE 158
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 114
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 157
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 161
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 28..45
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 47..53
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 89..101
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 105..108
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 127..136
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 149..162
FT /evidence="ECO:0007829|PDB:2OS0"
FT HELIX 167..170
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:2OS0"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:2OS0"
SQ SEQUENCE 187 AA; 20912 MW; 9CAF46335311B0B2 CRC64;
MITMKDIIRE GNPTLRAVAE EVPVPITEED RQLGEDMLTF LKNSQDPVKA EELQLRGGVG
LAAPQLDISK RIIAVHVPSN DPENETPSLS TVMYNPKILS HSVQDVCLGE GEGCLSVDRD
VPGYVVRHNK ITVSYFDMAG EKHKVRLKNY EAIVVQHEID HINGIMFYDH INKENPFALK
EGVLVIE
