ID DEF_STRR6 Reviewed; 203 AA. AC Q8DP79; DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot. DT 01-MAR-2003, sequence version 1. DT 27-MAR-2024, entry version 133. 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=spr1310; OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6). OC Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; OC Streptococcus. OX NCBI_TaxID=171101; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC BAA-255 / R6; RX PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001; RA Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S., RA DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C., RA Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J., RA Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M., RA McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B., RA Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y., RA Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R., RA Rosteck P.R. Jr., Skatrud P.L., Glass J.I.; RT "Genome of the bacterium Streptococcus pneumoniae strain R6."; RL J. Bacteriol. 183:5709-5717(2001). 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; AE007317; AAL00114.1; -; Genomic_DNA. DR PIR; E98035; E98035. DR RefSeq; NP_358903.1; NC_003098.1. DR RefSeq; WP_001272961.1; NC_003098.1. DR PDB; 2AI7; X-ray; 2.00 A; A=1-202. DR PDB; 2AIA; X-ray; 1.70 A; A=1-202. DR PDB; 2AIE; X-ray; 1.70 A; P=1-202. DR PDB; 3SVJ; X-ray; 1.55 A; P=1-203. DR PDB; 4EOX; X-ray; 1.78 A; P=1-203. DR PDB; 6OW2; X-ray; 1.70 A; P=2-203. DR PDB; 6OW7; X-ray; 1.45 A; P/Q=2-203. DR PDBsum; 2AI7; -. DR PDBsum; 2AIA; -. DR PDBsum; 2AIE; -. DR PDBsum; 3SVJ; -. DR PDBsum; 4EOX; -. DR PDBsum; 6OW2; -. DR PDBsum; 6OW7; -. DR AlphaFoldDB; Q8DP79; -. DR SMR; Q8DP79; -. DR STRING; 171101.spr1310; -. DR BindingDB; Q8DP79; -. DR DrugBank; DB08524; 2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE. DR DrugBank; DB08523; [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL. DR DrugBank; DB08525; HYDROXY[3-(6-METHYLPYRIDIN-2-YL)PROPYL]FORMAMIDE. DR GeneID; 66806556; -. DR KEGG; spr:spr1310; -. DR PATRIC; fig|171101.6.peg.1422; -. DR eggNOG; COG0242; Bacteria. DR HOGENOM; CLU_061901_4_0_9; -. DR EvolutionaryTrace; Q8DP79; -. DR PRO; PR:Q8DP79; -. DR Proteomes; UP000000586; Chromosome. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0042586; F:peptide deformylase activity; IBA:GO_Central. DR GO; GO:0043686; P:co-translational protein 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; 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..203 FT /note="Peptide deformylase" FT /id="PRO_0000082858" FT ACT_SITE 174 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 130 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 173 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 177 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:6OW7" FT HELIX 16..18 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 25..28 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 40..57 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 59..65 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 71..74 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 75..78 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 82..90 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 100..117 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 119..124 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 143..152 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 158..163 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 165..178 FT /evidence="ECO:0007829|PDB:6OW7" FT HELIX 183..186 FT /evidence="ECO:0007829|PDB:6OW7" FT STRAND 189..191 FT /evidence="ECO:0007829|PDB:4EOX" FT STRAND 199..202 FT /evidence="ECO:0007829|PDB:6OW7" SQ SEQUENCE 203 AA; 22692 MW; E332956982A67161 CRC64; MSAIERITKA AHLIDMNDII REGNPTLRTV AEEVTFPLSD QEIILGEKMM QFLKHSQDPV MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ EAYDLEAIMY NPKIVSHSVQ DAALGEGEGC LSVDRNVPGY VVRHARVTVD YFDKDGEKHR IKLKGYNSIV VQHEIDHING IMFYDRINEK DPFAVKDGLL ILE //