ID DEF_STRP1 Reviewed; 204 AA. AC P68771; P82590; Q48WI8; Q99XY7; DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot. DT 21-DEC-2004, sequence version 1. DT 27-MAR-2024, entry version 125. 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}; GN OrderedLocusNames=SPy_1958, M5005_Spy1669; OS Streptococcus pyogenes serotype M1. OC Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; OC Streptococcus. OX NCBI_TaxID=301447; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 700294 / SF370 / Serotype M1; RX PubMed=11296296; DOI=10.1073/pnas.071559398; RA Ferretti J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K., RA Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P., RA Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X., RA Clifton S.W., Roe B.A., McLaughlin R.E.; RT "Complete genome sequence of an M1 strain of Streptococcus pyogenes."; RL Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC BAA-947 / MGAS5005 / Serotype M1; RX PubMed=16088826; DOI=10.1086/432514; RA Sumby P., Porcella S.F., Madrigal A.G., Barbian K.D., Virtaneva K., RA Ricklefs S.M., Sturdevant D.E., Graham M.R., Vuopio-Varkila J., Hoe N.P., RA Musser J.M.; RT "Evolutionary origin and emergence of a highly successful clone of serotype RT M1 group A Streptococcus involved multiple horizontal gene transfer RT events."; RL J. Infect. Dis. 192:771-782(2005). 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; Evidence={ECO:0000255|HAMAP- CC 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE004092; AAK34651.1; -; Genomic_DNA. DR EMBL; CP000017; AAZ52287.1; -; Genomic_DNA. DR RefSeq; NP_269930.1; NC_002737.2. DR PDB; 2OS3; X-ray; 2.26 A; A=2-204. DR PDBsum; 2OS3; -. DR AlphaFoldDB; P68771; -. DR SMR; P68771; -. DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide. DR PaxDb; 1314-HKU360_01786; -. DR KEGG; spy:SPy_1958; -. DR KEGG; spz:M5005_Spy1669; -. DR PATRIC; fig|160490.10.peg.1705; -. DR HOGENOM; CLU_061901_4_0_9; -. DR OMA; HLYYDHI; -. DR EvolutionaryTrace; P68771; -. DR Proteomes; UP000000750; 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; 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:SF8; 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; Hydrolase; Iron; Metal-binding; Protein biosynthesis; KW Reference proteome. FT CHAIN 1..204 FT /note="Peptide deformylase" FT /id="PRO_0000082859" FT ACT_SITE 175 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 131 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 174 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 178 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT HELIX 3..7 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 16..18 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 25..28 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 40..56 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 59..65 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 71..74 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 75..78 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 82..90 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 101..118 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 120..125 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 144..153 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 159..164 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 166..178 FT /evidence="ECO:0007829|PDB:2OS3" FT TURN 179..181 FT /evidence="ECO:0007829|PDB:2OS3" FT HELIX 184..187 FT /evidence="ECO:0007829|PDB:2OS3" FT STRAND 200..203 FT /evidence="ECO:0007829|PDB:2OS3" SQ SEQUENCE 204 AA; 22862 MW; 89F8EDE94D94DC05 CRC64; MSAQDKLIKP SHLITMDDII REGNPTLRAV AKEVSLPLCD EDILLGEKMM QFLKHSQDPV MAEKLGLRAG VGLAAPQIDV SKRIIAVLVP NLPDKEGNPP KEAYSWQEVL YNPKIVSHSV QDAALSDGEG CLSVDRVVEG YVVRHARVTV DYYDKEGQQH RIKLKGYNAI VVQHEIDHIN GVLFYDRINA KNPFETKEEL LILD //